diff --git a/x-pack/plugins/lens/common/types.ts b/x-pack/plugins/lens/common/types.ts
index 56a56bdc2d59c..c572b59899fce 100644
--- a/x-pack/plugins/lens/common/types.ts
+++ b/x-pack/plugins/lens/common/types.ts
@@ -4,6 +4,8 @@
  * you may not use this file except in compliance with the Elastic License.
  */
 
+import { FilterMeta, Filter } from 'src/plugins/data/common';
+
 export interface ExistingFields {
   indexPatternTitle: string;
   existingFieldNames: string[];
@@ -13,3 +15,11 @@ export interface DateRange {
   fromDate: string;
   toDate: string;
 }
+
+export interface PersistableFilterMeta extends FilterMeta {
+  indexRefName?: string;
+}
+
+export interface PersistableFilter extends Filter {
+  meta: PersistableFilterMeta;
+}
diff --git a/x-pack/plugins/lens/public/app_plugin/app.test.tsx b/x-pack/plugins/lens/public/app_plugin/app.test.tsx
index 70136a486e8c1..442f82161512f 100644
--- a/x-pack/plugins/lens/public/app_plugin/app.test.tsx
+++ b/x-pack/plugins/lens/public/app_plugin/app.test.tsx
@@ -33,7 +33,7 @@ import { navigationPluginMock } from '../../../../../src/plugins/navigation/publ
 import { TopNavMenuData } from '../../../../../src/plugins/navigation/public';
 import { coreMock } from 'src/core/public/mocks';
 
-jest.mock('../persistence');
+jest.mock('../editor_frame_service/editor_frame/expression_helpers');
 jest.mock('src/core/public');
 jest.mock('../../../../../src/plugins/saved_objects/public', () => {
   // eslint-disable-next-line no-shadow
@@ -284,11 +284,11 @@ describe('Lens App', () => {
     (defaultArgs.docStorage.load as jest.Mock).mockResolvedValue({
       id: '1234',
       title: 'Daaaaaaadaumching!',
-      expression: 'valid expression',
       state: {
         query: 'fake query',
-        datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
+        filters: [],
       },
+      references: [],
     });
     await act(async () => {
       instance.setProps({ docId: '1234' });
@@ -346,12 +346,11 @@ describe('Lens App', () => {
       args.editorFrame = frame;
       (args.docStorage.load as jest.Mock).mockResolvedValue({
         id: '1234',
-        expression: 'valid expression',
         state: {
           query: 'fake query',
           filters: [{ query: { match_phrase: { src: 'test' } } }],
-          datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
         },
+        references: [{ type: 'index-pattern', id: '1', name: 'index-pattern-0' }],
       });
 
       instance = mount(<App {...args} />);
@@ -375,15 +374,13 @@ describe('Lens App', () => {
       expect(frame.mount).toHaveBeenCalledWith(
         expect.any(Element),
         expect.objectContaining({
-          doc: {
+          doc: expect.objectContaining({
             id: '1234',
-            expression: 'valid expression',
-            state: {
+            state: expect.objectContaining({
               query: 'fake query',
               filters: [{ query: { match_phrase: { src: 'test' } } }],
-              datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
-            },
-          },
+            }),
+          }),
         })
       );
     });
@@ -444,7 +441,6 @@ describe('Lens App', () => {
           expression: 'valid expression',
           state: {
             query: 'kuery',
-            datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
           },
         } as jest.ResolvedValue<Document>);
       });
@@ -467,7 +463,12 @@ describe('Lens App', () => {
       }
 
       async function save({
-        lastKnownDoc = { expression: 'kibana 3' },
+        lastKnownDoc = {
+          references: [],
+          state: {
+            filters: [],
+          },
+        },
         initialDocId,
         ...saveProps
       }: SaveProps & {
@@ -481,16 +482,14 @@ describe('Lens App', () => {
         args.editorFrame = frame;
         (args.docStorage.load as jest.Mock).mockResolvedValue({
           id: '1234',
-          expression: 'kibana',
+          references: [],
           state: {
             query: 'fake query',
-            datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
             filters: [],
           },
         });
         (args.docStorage.save as jest.Mock).mockImplementation(async ({ id }) => ({
           id: id || 'aaa',
-          expression: 'kibana 2',
         }));
 
         await act(async () => {
@@ -508,6 +507,7 @@ describe('Lens App', () => {
           onChange({
             filterableIndexPatterns: [],
             doc: { id: initialDocId, ...lastKnownDoc } as Document,
+            isSaveable: true,
           })
         );
 
@@ -541,7 +541,8 @@ describe('Lens App', () => {
         act(() =>
           onChange({
             filterableIndexPatterns: [],
-            doc: ({ id: 'will save this', expression: 'valid expression' } as unknown) as Document,
+            doc: ({ id: 'will save this' } as unknown) as Document,
+            isSaveable: true,
           })
         );
         instance.update();
@@ -560,7 +561,8 @@ describe('Lens App', () => {
         act(() =>
           onChange({
             filterableIndexPatterns: [],
-            doc: ({ id: 'will save this', expression: 'valid expression' } as unknown) as Document,
+            doc: ({ id: 'will save this' } as unknown) as Document,
+            isSaveable: true,
           })
         );
         instance.update();
@@ -575,11 +577,12 @@ describe('Lens App', () => {
           newTitle: 'hello there',
         });
 
-        expect(args.docStorage.save).toHaveBeenCalledWith({
-          id: undefined,
-          title: 'hello there',
-          expression: 'kibana 3',
-        });
+        expect(args.docStorage.save).toHaveBeenCalledWith(
+          expect.objectContaining({
+            id: undefined,
+            title: 'hello there',
+          })
+        );
 
         expect(args.redirectTo).toHaveBeenCalledWith('aaa', undefined, true);
 
@@ -595,11 +598,12 @@ describe('Lens App', () => {
           newTitle: 'hello there',
         });
 
-        expect(args.docStorage.save).toHaveBeenCalledWith({
-          id: undefined,
-          title: 'hello there',
-          expression: 'kibana 3',
-        });
+        expect(args.docStorage.save).toHaveBeenCalledWith(
+          expect.objectContaining({
+            id: undefined,
+            title: 'hello there',
+          })
+        );
 
         expect(args.redirectTo).toHaveBeenCalledWith('aaa', undefined, true);
 
@@ -615,11 +619,12 @@ describe('Lens App', () => {
           newTitle: 'hello there',
         });
 
-        expect(args.docStorage.save).toHaveBeenCalledWith({
-          id: '1234',
-          title: 'hello there',
-          expression: 'kibana 3',
-        });
+        expect(args.docStorage.save).toHaveBeenCalledWith(
+          expect.objectContaining({
+            id: '1234',
+            title: 'hello there',
+          })
+        );
 
         expect(args.redirectTo).not.toHaveBeenCalled();
 
@@ -639,7 +644,8 @@ describe('Lens App', () => {
         act(() =>
           onChange({
             filterableIndexPatterns: [],
-            doc: ({ id: undefined, expression: 'new expression' } as unknown) as Document,
+            doc: ({ id: undefined } as unknown) as Document,
+            isSaveable: true,
           })
         );
 
@@ -663,11 +669,12 @@ describe('Lens App', () => {
           newTitle: 'hello there',
         });
 
-        expect(args.docStorage.save).toHaveBeenCalledWith({
-          expression: 'kibana 3',
-          id: undefined,
-          title: 'hello there',
-        });
+        expect(args.docStorage.save).toHaveBeenCalledWith(
+          expect.objectContaining({
+            id: undefined,
+            title: 'hello there',
+          })
+        );
 
         expect(args.redirectTo).toHaveBeenCalledWith('aaa', true, true);
       });
@@ -717,7 +724,8 @@ describe('Lens App', () => {
         await act(async () =>
           onChange({
             filterableIndexPatterns: [],
-            doc: ({ id: '123', expression: 'valid expression' } as unknown) as Document,
+            doc: ({ id: '123' } as unknown) as Document,
+            isSaveable: true,
           })
         );
         instance.update();
@@ -756,7 +764,8 @@ describe('Lens App', () => {
         await act(async () =>
           onChange({
             filterableIndexPatterns: [],
-            doc: ({ expression: 'valid expression' } as unknown) as Document,
+            doc: ({} as unknown) as Document,
+            isSaveable: true,
           })
         );
         instance.update();
@@ -779,7 +788,6 @@ describe('Lens App', () => {
         expression: 'valid expression',
         state: {
           query: 'kuery',
-          datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
         },
       } as jest.ResolvedValue<Document>);
     });
@@ -824,8 +832,9 @@ describe('Lens App', () => {
 
       await act(async () => {
         onChange({
-          filterableIndexPatterns: [{ id: '1', title: 'newIndex' }],
-          doc: ({ id: undefined, expression: 'valid expression' } as unknown) as Document,
+          filterableIndexPatterns: ['1'],
+          doc: ({ id: undefined } as unknown) as Document,
+          isSaveable: true,
         });
       });
 
@@ -842,8 +851,9 @@ describe('Lens App', () => {
 
       await act(async () => {
         onChange({
-          filterableIndexPatterns: [{ id: '2', title: 'second index' }],
-          doc: ({ id: undefined, expression: 'valid expression' } as unknown) as Document,
+          filterableIndexPatterns: ['2'],
+          doc: ({ id: undefined } as unknown) as Document,
+          isSaveable: true,
         });
       });
 
@@ -1078,11 +1088,11 @@ describe('Lens App', () => {
       (defaultArgs.docStorage.load as jest.Mock).mockResolvedValue({
         id: '1234',
         title: 'My cool doc',
-        expression: 'valid expression',
         state: {
           query: 'kuery',
-          datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'saved' }] },
+          filters: [],
         },
+        references: [],
       } as jest.ResolvedValue<Document>);
     });
 
@@ -1114,7 +1124,12 @@ describe('Lens App', () => {
       act(() =>
         onChange({
           filterableIndexPatterns: [],
-          doc: ({ id: undefined, expression: 'valid expression' } as unknown) as Document,
+          doc: ({
+            id: undefined,
+
+            references: [],
+          } as unknown) as Document,
+          isSaveable: true,
         })
       );
       instance.update();
@@ -1135,7 +1150,8 @@ describe('Lens App', () => {
       act(() =>
         onChange({
           filterableIndexPatterns: [],
-          doc: ({ id: undefined, expression: 'valid expression' } as unknown) as Document,
+          doc: ({ id: undefined, state: {} } as unknown) as Document,
+          isSaveable: true,
         })
       );
       instance.update();
@@ -1159,7 +1175,12 @@ describe('Lens App', () => {
       act(() =>
         onChange({
           filterableIndexPatterns: [],
-          doc: ({ id: '1234', expression: 'different expression' } as unknown) as Document,
+          doc: ({
+            id: '1234',
+
+            references: [],
+          } as unknown) as Document,
+          isSaveable: true,
         })
       );
       instance.update();
@@ -1183,7 +1204,16 @@ describe('Lens App', () => {
       act(() =>
         onChange({
           filterableIndexPatterns: [],
-          doc: ({ id: '1234', expression: 'valid expression' } as unknown) as Document,
+          doc: ({
+            id: '1234',
+            title: 'My cool doc',
+            references: [],
+            state: {
+              query: 'kuery',
+              filters: [],
+            },
+          } as unknown) as Document,
+          isSaveable: true,
         })
       );
       instance.update();
@@ -1207,7 +1237,8 @@ describe('Lens App', () => {
       act(() =>
         onChange({
           filterableIndexPatterns: [],
-          doc: ({ id: '1234', expression: null } as unknown) as Document,
+          doc: ({ id: '1234', references: [] } as unknown) as Document,
+          isSaveable: true,
         })
       );
       instance.update();
diff --git a/x-pack/plugins/lens/public/app_plugin/app.tsx b/x-pack/plugins/lens/public/app_plugin/app.tsx
index 5ca6f27a0c578..021ca8b182b2b 100644
--- a/x-pack/plugins/lens/public/app_plugin/app.tsx
+++ b/x-pack/plugins/lens/public/app_plugin/app.tsx
@@ -28,7 +28,7 @@ import {
   OnSaveProps,
   checkForDuplicateTitle,
 } from '../../../../../src/plugins/saved_objects/public';
-import { Document, SavedObjectStore } from '../persistence';
+import { Document, SavedObjectStore, injectFilterReferences } from '../persistence';
 import { EditorFrameInstance } from '../types';
 import { NativeRenderer } from '../native_renderer';
 import { trackUiEvent } from '../lens_ui_telemetry';
@@ -57,6 +57,7 @@ interface State {
   query: Query;
   filters: Filter[];
   savedQuery?: SavedQuery;
+  isSaveable: boolean;
 }
 
 export function App({
@@ -100,6 +101,7 @@ export function App({
       originatingApp,
       filters: data.query.filterManager.getFilters(),
       indicateNoData: false,
+      isSaveable: false,
     };
   });
 
@@ -122,11 +124,7 @@ export function App({
 
   const { lastKnownDoc } = state;
 
-  const isSaveable =
-    lastKnownDoc &&
-    lastKnownDoc.expression &&
-    lastKnownDoc.expression.length > 0 &&
-    core.application.capabilities.visualize.save;
+  const savingPermitted = state.isSaveable && core.application.capabilities.visualize.save;
 
   useEffect(() => {
     // Clear app-specific filters when navigating to Lens. Necessary because Lens
@@ -177,15 +175,34 @@ export function App({
     history,
   ]);
 
+  const getLastKnownDocWithoutPinnedFilters = useCallback(
+    function () {
+      if (!lastKnownDoc) return undefined;
+      const [pinnedFilters, appFilters] = _.partition(
+        injectFilterReferences(lastKnownDoc.state?.filters || [], lastKnownDoc.references),
+        esFilters.isFilterPinned
+      );
+      return pinnedFilters?.length
+        ? {
+            ...lastKnownDoc,
+            state: {
+              ...lastKnownDoc.state,
+              filters: appFilters,
+            },
+          }
+        : lastKnownDoc;
+    },
+    [lastKnownDoc]
+  );
+
   useEffect(() => {
     onAppLeave((actions) => {
       // Confirm when the user has made any changes to an existing doc
       // or when the user has configured something without saving
       if (
         core.application.capabilities.visualize.save &&
-        (state.persistedDoc?.expression
-          ? !_.isEqual(lastKnownDoc?.expression, state.persistedDoc.expression)
-          : lastKnownDoc?.expression)
+        !_.isEqual(state.persistedDoc?.state, getLastKnownDocWithoutPinnedFilters()?.state) &&
+        (state.isSaveable || state.persistedDoc)
       ) {
         return actions.confirm(
           i18n.translate('xpack.lens.app.unsavedWorkMessage', {
@@ -199,7 +216,14 @@ export function App({
         return actions.default();
       }
     });
-  }, [lastKnownDoc, onAppLeave, state.persistedDoc, core.application.capabilities.visualize.save]);
+  }, [
+    lastKnownDoc,
+    onAppLeave,
+    state.persistedDoc,
+    state.isSaveable,
+    core.application.capabilities.visualize.save,
+    getLastKnownDocWithoutPinnedFilters,
+  ]);
 
   // Sync Kibana breadcrumbs any time the saved document's title changes
   useEffect(() => {
@@ -248,13 +272,17 @@ export function App({
           .load(docId)
           .then((doc) => {
             getAllIndexPatterns(
-              doc.state.datasourceMetaData.filterableIndexPatterns,
+              _.uniq(
+                doc.references.filter(({ type }) => type === 'index-pattern').map(({ id }) => id)
+              ),
               data.indexPatterns,
               core.notifications
             )
               .then((indexPatterns) => {
                 // Don't overwrite any pinned filters
-                data.query.filterManager.setAppFilters(doc.state.filters);
+                data.query.filterManager.setAppFilters(
+                  injectFilterReferences(doc.state.filters, doc.references)
+                );
                 setState((s) => ({
                   ...s,
                   isLoading: false,
@@ -264,13 +292,13 @@ export function App({
                   indexPatternsForTopNav: indexPatterns,
                 }));
               })
-              .catch(() => {
+              .catch((e) => {
                 setState((s) => ({ ...s, isLoading: false }));
 
                 redirectTo();
               });
           })
-          .catch(() => {
+          .catch((e) => {
             setState((s) => ({ ...s, isLoading: false }));
 
             core.notifications.toasts.addDanger(
@@ -306,22 +334,9 @@ export function App({
     if (!lastKnownDoc) {
       return;
     }
-    const [pinnedFilters, appFilters] = _.partition(
-      lastKnownDoc.state?.filters,
-      esFilters.isFilterPinned
-    );
-    const lastDocWithoutPinned = pinnedFilters?.length
-      ? {
-          ...lastKnownDoc,
-          state: {
-            ...lastKnownDoc.state,
-            filters: appFilters,
-          },
-        }
-      : lastKnownDoc;
 
     const doc = {
-      ...lastDocWithoutPinned,
+      ...getLastKnownDocWithoutPinnedFilters()!,
       description: saveProps.newDescription,
       id: saveProps.newCopyOnSave ? undefined : lastKnownDoc.id,
       title: saveProps.newTitle,
@@ -411,7 +426,7 @@ export function App({
                         emphasize: true,
                         iconType: 'check',
                         run: () => {
-                          if (isSaveable && lastKnownDoc) {
+                          if (savingPermitted) {
                             runSave({
                               newTitle: lastKnownDoc.title,
                               newCopyOnSave: false,
@@ -421,7 +436,7 @@ export function App({
                           }
                         },
                         testId: 'lnsApp_saveAndReturnButton',
-                        disableButton: !isSaveable,
+                        disableButton: !savingPermitted,
                       },
                     ]
                   : []),
@@ -436,12 +451,12 @@ export function App({
                         }),
                   emphasize: !state.originatingApp || !lastKnownDoc?.id,
                   run: () => {
-                    if (isSaveable && lastKnownDoc) {
+                    if (savingPermitted) {
                       setState((s) => ({ ...s, isSaveModalVisible: true }));
                     }
                   },
                   testId: 'lnsApp_saveButton',
-                  disableButton: !isSaveable,
+                  disableButton: !savingPermitted,
                 },
               ]}
               data-test-subj="lnsApp_topNav"
@@ -522,7 +537,10 @@ export function App({
                 doc: state.persistedDoc,
                 onError,
                 showNoDataPopover,
-                onChange: ({ filterableIndexPatterns, doc }) => {
+                onChange: ({ filterableIndexPatterns, doc, isSaveable }) => {
+                  if (isSaveable !== state.isSaveable) {
+                    setState((s) => ({ ...s, isSaveable }));
+                  }
                   if (!_.isEqual(state.persistedDoc, doc)) {
                     setState((s) => ({ ...s, lastKnownDoc: doc }));
                   }
@@ -530,8 +548,8 @@ export function App({
                   // Update the cached index patterns if the user made a change to any of them
                   if (
                     state.indexPatternsForTopNav.length !== filterableIndexPatterns.length ||
-                    filterableIndexPatterns.find(
-                      ({ id }) =>
+                    filterableIndexPatterns.some(
+                      (id) =>
                         !state.indexPatternsForTopNav.find((indexPattern) => indexPattern.id === id)
                     )
                   ) {
@@ -573,12 +591,12 @@ export function App({
 }
 
 export async function getAllIndexPatterns(
-  ids: Array<{ id: string }>,
+  ids: string[],
   indexPatternsService: IndexPatternsContract,
   notifications: NotificationsStart
 ): Promise<IndexPatternInstance[]> {
   try {
-    return await Promise.all(ids.map(({ id }) => indexPatternsService.get(id)));
+    return await Promise.all(ids.map((id) => indexPatternsService.get(id)));
   } catch (e) {
     notifications.toasts.addDanger(
       i18n.translate('xpack.lens.app.indexPatternLoadingError', {
diff --git a/x-pack/plugins/lens/public/datatable_visualization/visualization.test.tsx b/x-pack/plugins/lens/public/datatable_visualization/visualization.test.tsx
index 0b6584277ffa7..194f12cf9291b 100644
--- a/x-pack/plugins/lens/public/datatable_visualization/visualization.test.tsx
+++ b/x-pack/plugins/lens/public/datatable_visualization/visualization.test.tsx
@@ -50,20 +50,6 @@ describe('Datatable Visualization', () => {
     });
   });
 
-  describe('#getPersistableState', () => {
-    it('should persist the internal state', () => {
-      const expectedState: DatatableVisualizationState = {
-        layers: [
-          {
-            layerId: 'baz',
-            columns: ['a', 'b', 'c'],
-          },
-        ],
-      };
-      expect(datatableVisualization.getPersistableState(expectedState)).toEqual(expectedState);
-    });
-  });
-
   describe('#getLayerIds', () => {
     it('return the layer ids', () => {
       const state: DatatableVisualizationState = {
@@ -340,7 +326,10 @@ describe('Datatable Visualization', () => {
         label: 'label',
       });
 
-      const expression = datatableVisualization.toExpression({ layers: [layer] }, frame) as Ast;
+      const expression = datatableVisualization.toExpression(
+        { layers: [layer] },
+        frame.datasourceLayers
+      ) as Ast;
       const tableArgs = buildExpression(expression).findFunction('lens_datatable_columns');
 
       expect(tableArgs).toHaveLength(1);
diff --git a/x-pack/plugins/lens/public/datatable_visualization/visualization.tsx b/x-pack/plugins/lens/public/datatable_visualization/visualization.tsx
index 659f8ea12bcb0..5aff4e14b17f2 100644
--- a/x-pack/plugins/lens/public/datatable_visualization/visualization.tsx
+++ b/x-pack/plugins/lens/public/datatable_visualization/visualization.tsx
@@ -25,10 +25,7 @@ function newLayerState(layerId: string): LayerState {
   };
 }
 
-export const datatableVisualization: Visualization<
-  DatatableVisualizationState,
-  DatatableVisualizationState
-> = {
+export const datatableVisualization: Visualization<DatatableVisualizationState> = {
   id: 'lnsDatatable',
 
   visualizationTypes: [
@@ -75,8 +72,6 @@ export const datatableVisualization: Visualization<
     );
   },
 
-  getPersistableState: (state) => state,
-
   getSuggestions({
     table,
     state,
@@ -186,9 +181,9 @@ export const datatableVisualization: Visualization<
     };
   },
 
-  toExpression(state, frame): Ast {
+  toExpression(state, datasourceLayers): Ast {
     const layer = state.layers[0];
-    const datasource = frame.datasourceLayers[layer.layerId];
+    const datasource = datasourceLayers[layer.layerId];
     const originalOrder = datasource.getTableSpec().map(({ columnId }) => columnId);
     // When we add a column it could be empty, and therefore have no order
     const sortedColumns = Array.from(new Set(originalOrder.concat(layer.columns)));
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/__mocks__/expression_helpers.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/__mocks__/expression_helpers.ts
new file mode 100644
index 0000000000000..e0b3616315cbd
--- /dev/null
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/__mocks__/expression_helpers.ts
@@ -0,0 +1,14 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License;
+ * you may not use this file except in compliance with the Elastic License.
+ */
+
+import { Ast } from '@kbn/interpreter/common';
+
+export function buildExpression(): Ast {
+  return {
+    type: 'expression',
+    chain: [{ type: 'function', function: 'test', arguments: {} }],
+  };
+}
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/config_panel/layer_panel.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/config_panel/layer_panel.tsx
index 38224bf962a3f..b2804cfddba58 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/config_panel/layer_panel.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/config_panel/layer_panel.tsx
@@ -124,7 +124,6 @@ export function LayerPanel(
                     const nextPublicAPI = layerDatasource.getPublicAPI({
                       state: newState,
                       layerId,
-                      dateRange: props.framePublicAPI.dateRange,
                     });
                     const nextTable = new Set(
                       nextPublicAPI.getTableSpec().map(({ columnId }) => columnId)
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.test.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.test.tsx
index 2f7a78197b2b2..e628ea0675a8d 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.test.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.test.tsx
@@ -170,25 +170,22 @@ describe('editor_frame', () => {
             doc={{
               visualizationType: 'testVis',
               title: '',
-              expression: '',
               state: {
                 datasourceStates: {
                   testDatasource: datasource1State,
                   testDatasource2: datasource2State,
                 },
                 visualization: {},
-                datasourceMetaData: {
-                  filterableIndexPatterns: [],
-                },
                 query: { query: '', language: 'lucene' },
                 filters: [],
               },
+              references: [],
             }}
           />
         );
       });
-      expect(mockDatasource.initialize).toHaveBeenCalledWith(datasource1State);
-      expect(mockDatasource2.initialize).toHaveBeenCalledWith(datasource2State);
+      expect(mockDatasource.initialize).toHaveBeenCalledWith(datasource1State, []);
+      expect(mockDatasource2.initialize).toHaveBeenCalledWith(datasource2State, []);
       expect(mockDatasource3.initialize).not.toHaveBeenCalled();
     });
 
@@ -425,21 +422,6 @@ describe('editor_frame', () => {
               "function": "kibana",
               "type": "function",
             },
-            Object {
-              "arguments": Object {
-                "filters": Array [
-                  "[]",
-                ],
-                "query": Array [
-                  "{\\"query\\":\\"\\",\\"language\\":\\"lucene\\"}",
-                ],
-                "timeRange": Array [
-                  "{\\"from\\":\\"\\",\\"to\\":\\"\\"}",
-                ],
-              },
-              "function": "kibana_context",
-              "type": "function",
-            },
             Object {
               "arguments": Object {
                 "layerIds": Array [
@@ -499,19 +481,16 @@ describe('editor_frame', () => {
             doc={{
               visualizationType: 'testVis',
               title: '',
-              expression: '',
               state: {
                 datasourceStates: {
                   testDatasource: {},
                   testDatasource2: {},
                 },
                 visualization: {},
-                datasourceMetaData: {
-                  filterableIndexPatterns: [],
-                },
                 query: { query: '', language: 'lucene' },
                 filters: [],
               },
+              references: [],
             }}
           />
         );
@@ -535,21 +514,6 @@ describe('editor_frame', () => {
               "function": "kibana",
               "type": "function",
             },
-            Object {
-              "arguments": Object {
-                "filters": Array [
-                  "[]",
-                ],
-                "query": Array [
-                  "{\\"query\\":\\"\\",\\"language\\":\\"lucene\\"}",
-                ],
-                "timeRange": Array [
-                  "{\\"from\\":\\"\\",\\"to\\":\\"\\"}",
-                ],
-              },
-              "function": "kibana_context",
-              "type": "function",
-            },
             Object {
               "arguments": Object {
                 "layerIds": Array [
@@ -747,19 +711,16 @@ describe('editor_frame', () => {
             doc={{
               visualizationType: 'testVis',
               title: '',
-              expression: '',
               state: {
                 datasourceStates: {
                   testDatasource: {},
                   testDatasource2: {},
                 },
                 visualization: {},
-                datasourceMetaData: {
-                  filterableIndexPatterns: [],
-                },
                 query: { query: '', language: 'lucene' },
                 filters: [],
               },
+              references: [],
             }}
           />
         );
@@ -802,19 +763,16 @@ describe('editor_frame', () => {
             doc={{
               visualizationType: 'testVis',
               title: '',
-              expression: '',
               state: {
                 datasourceStates: {
                   testDatasource: datasource1State,
                   testDatasource2: datasource2State,
                 },
                 visualization: {},
-                datasourceMetaData: {
-                  filterableIndexPatterns: [],
-                },
                 query: { query: '', language: 'lucene' },
                 filters: [],
               },
+              references: [],
             }}
           />
         );
@@ -842,7 +800,6 @@ describe('editor_frame', () => {
 
     it('should give access to the datasource state in the datasource factory function', async () => {
       const datasourceState = {};
-      const dateRange = { fromDate: 'now-1w', toDate: 'now' };
       mockDatasource.initialize.mockResolvedValue(datasourceState);
       mockDatasource.getLayers.mockReturnValue(['first']);
 
@@ -850,7 +807,6 @@ describe('editor_frame', () => {
         mount(
           <EditorFrame
             {...getDefaultProps()}
-            dateRange={dateRange}
             visualizationMap={{
               testVis: mockVisualization,
             }}
@@ -865,7 +821,6 @@ describe('editor_frame', () => {
       });
 
       expect(mockDatasource.getPublicAPI).toHaveBeenCalledWith({
-        dateRange,
         state: datasourceState,
         layerId: 'first',
       });
@@ -1460,9 +1415,10 @@ describe('editor_frame', () => {
         })
       );
       mockDatasource.getLayers.mockReturnValue(['first']);
-      mockDatasource.getMetaData.mockReturnValue({
-        filterableIndexPatterns: [{ id: '1', title: 'resolved' }],
-      });
+      mockDatasource.getPersistableState = jest.fn((x) => ({
+        state: x,
+        savedObjectReferences: [{ type: 'index-pattern', id: '1', name: 'index-pattern-0' }],
+      }));
       mockVisualization.initialize.mockReturnValue({ initialState: true });
 
       await act(async () => {
@@ -1487,14 +1443,20 @@ describe('editor_frame', () => {
 
       expect(onChange).toHaveBeenCalledTimes(2);
       expect(onChange).toHaveBeenNthCalledWith(1, {
-        filterableIndexPatterns: [{ id: '1', title: 'resolved' }],
+        filterableIndexPatterns: ['1'],
         doc: {
-          expression: '',
           id: undefined,
+          description: undefined,
+          references: [
+            {
+              id: '1',
+              name: 'index-pattern-0',
+              type: 'index-pattern',
+            },
+          ],
           state: {
             visualization: null, // Not yet loaded
-            datasourceMetaData: { filterableIndexPatterns: [{ id: '1', title: 'resolved' }] },
-            datasourceStates: { testDatasource: undefined },
+            datasourceStates: { testDatasource: {} },
             query: { query: '', language: 'lucene' },
             filters: [],
           },
@@ -1502,18 +1464,23 @@ describe('editor_frame', () => {
           type: 'lens',
           visualizationType: 'testVis',
         },
+        isSaveable: false,
       });
       expect(onChange).toHaveBeenLastCalledWith({
-        filterableIndexPatterns: [{ id: '1', title: 'resolved' }],
+        filterableIndexPatterns: ['1'],
         doc: {
-          expression: '',
+          references: [
+            {
+              id: '1',
+              name: 'index-pattern-0',
+              type: 'index-pattern',
+            },
+          ],
+          description: undefined,
           id: undefined,
           state: {
             visualization: { initialState: true }, // Now loaded
-            datasourceMetaData: {
-              filterableIndexPatterns: [{ id: '1', title: 'resolved' }],
-            },
-            datasourceStates: { testDatasource: undefined },
+            datasourceStates: { testDatasource: {} },
             query: { query: '', language: 'lucene' },
             filters: [],
           },
@@ -1521,6 +1488,7 @@ describe('editor_frame', () => {
           type: 'lens',
           visualizationType: 'testVis',
         },
+        isSaveable: false,
       });
     });
 
@@ -1562,11 +1530,10 @@ describe('editor_frame', () => {
       expect(onChange).toHaveBeenNthCalledWith(3, {
         filterableIndexPatterns: [],
         doc: {
-          expression: expect.stringContaining('vis "expression"'),
           id: undefined,
+          references: [],
           state: {
-            datasourceMetaData: { filterableIndexPatterns: [] },
-            datasourceStates: { testDatasource: undefined },
+            datasourceStates: { testDatasource: { datasource: '' } },
             visualization: { initialState: true },
             query: { query: 'new query', language: 'lucene' },
             filters: [],
@@ -1575,6 +1542,7 @@ describe('editor_frame', () => {
           type: 'lens',
           visualizationType: 'testVis',
         },
+        isSaveable: true,
       });
     });
 
@@ -1583,9 +1551,10 @@ describe('editor_frame', () => {
 
       mockDatasource.initialize.mockResolvedValue({});
       mockDatasource.getLayers.mockReturnValue(['first']);
-      mockDatasource.getMetaData.mockReturnValue({
-        filterableIndexPatterns: [{ id: '1', title: 'resolved' }],
-      });
+      mockDatasource.getPersistableState = jest.fn((x) => ({
+        state: x,
+        savedObjectReferences: [{ type: 'index-pattern', id: '1', name: '' }],
+      }));
       mockVisualization.initialize.mockReturnValue({ initialState: true });
 
       await act(async () => {
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.tsx
index 48a3511a8f359..72ad8e074226c 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/editor_frame.tsx
@@ -7,13 +7,7 @@
 import React, { useEffect, useReducer } from 'react';
 import { CoreSetup, CoreStart } from 'kibana/public';
 import { ReactExpressionRendererType } from '../../../../../../src/plugins/expressions/public';
-import {
-  Datasource,
-  DatasourcePublicAPI,
-  FramePublicAPI,
-  Visualization,
-  DatasourceMetaData,
-} from '../../types';
+import { Datasource, FramePublicAPI, Visualization } from '../../types';
 import { reducer, getInitialState } from './state_management';
 import { DataPanelWrapper } from './data_panel_wrapper';
 import { ConfigPanelWrapper } from './config_panel';
@@ -26,6 +20,7 @@ import { getSavedObjectFormat } from './save';
 import { generateId } from '../../id_generator';
 import { Filter, Query, SavedQuery } from '../../../../../../src/plugins/data/public';
 import { EditorFrameStartPlugins } from '../service';
+import { initializeDatasources, createDatasourceLayers } from './state_helpers';
 
 export interface EditorFrameProps {
   doc?: Document;
@@ -45,8 +40,9 @@ export interface EditorFrameProps {
   filters: Filter[];
   savedQuery?: SavedQuery;
   onChange: (arg: {
-    filterableIndexPatterns: DatasourceMetaData['filterableIndexPatterns'];
+    filterableIndexPatterns: string[];
     doc: Document;
+    isSaveable: boolean;
   }) => void;
   showNoDataPopover: () => void;
 }
@@ -67,25 +63,19 @@ export function EditorFrame(props: EditorFrameProps) {
       // prevents executing dispatch on unmounted component
       let isUnmounted = false;
       if (!allLoaded) {
-        Object.entries(props.datasourceMap).forEach(([datasourceId, datasource]) => {
-          if (
-            state.datasourceStates[datasourceId] &&
-            state.datasourceStates[datasourceId].isLoading
-          ) {
-            datasource
-              .initialize(state.datasourceStates[datasourceId].state || undefined)
-              .then((datasourceState) => {
-                if (!isUnmounted) {
-                  dispatch({
-                    type: 'UPDATE_DATASOURCE_STATE',
-                    updater: datasourceState,
-                    datasourceId,
-                  });
-                }
-              })
-              .catch(onError);
-          }
-        });
+        initializeDatasources(props.datasourceMap, state.datasourceStates, props.doc?.references)
+          .then((result) => {
+            if (!isUnmounted) {
+              Object.entries(result).forEach(([datasourceId, { state: datasourceState }]) => {
+                dispatch({
+                  type: 'UPDATE_DATASOURCE_STATE',
+                  updater: datasourceState,
+                  datasourceId,
+                });
+              });
+            }
+          })
+          .catch(onError);
       }
       return () => {
         isUnmounted = true;
@@ -95,22 +85,7 @@ export function EditorFrame(props: EditorFrameProps) {
     [allLoaded, onError]
   );
 
-  const datasourceLayers: Record<string, DatasourcePublicAPI> = {};
-  Object.keys(props.datasourceMap)
-    .filter((id) => state.datasourceStates[id] && !state.datasourceStates[id].isLoading)
-    .forEach((id) => {
-      const datasourceState = state.datasourceStates[id].state;
-      const datasource = props.datasourceMap[id];
-
-      const layers = datasource.getLayers(datasourceState);
-      layers.forEach((layer) => {
-        datasourceLayers[layer] = props.datasourceMap[id].getPublicAPI({
-          state: datasourceState,
-          layerId: layer,
-          dateRange: props.dateRange,
-        });
-      });
-    });
+  const datasourceLayers = createDatasourceLayers(props.datasourceMap, state.datasourceStates);
 
   const framePublicAPI: FramePublicAPI = {
     datasourceLayers,
@@ -165,7 +140,18 @@ export function EditorFrame(props: EditorFrameProps) {
       if (props.doc) {
         dispatch({
           type: 'VISUALIZATION_LOADED',
-          doc: props.doc,
+          doc: {
+            ...props.doc,
+            state: {
+              ...props.doc.state,
+              visualization: props.doc.visualizationType
+                ? props.visualizationMap[props.doc.visualizationType].initialize(
+                    framePublicAPI,
+                    props.doc.state.visualization
+                  )
+                : props.doc.state.visualization,
+            },
+          },
         });
       } else {
         dispatch({
@@ -206,36 +192,20 @@ export function EditorFrame(props: EditorFrameProps) {
         return;
       }
 
-      const indexPatterns: DatasourceMetaData['filterableIndexPatterns'] = [];
-      Object.entries(props.datasourceMap)
-        .filter(([id, datasource]) => {
-          const stateWrapper = state.datasourceStates[id];
-          return (
-            stateWrapper &&
-            !stateWrapper.isLoading &&
-            datasource.getLayers(stateWrapper.state).length > 0
-          );
+      props.onChange(
+        getSavedObjectFormat({
+          activeDatasources: Object.keys(state.datasourceStates).reduce(
+            (datasourceMap, datasourceId) => ({
+              ...datasourceMap,
+              [datasourceId]: props.datasourceMap[datasourceId],
+            }),
+            {}
+          ),
+          visualization: activeVisualization,
+          state,
+          framePublicAPI,
         })
-        .forEach(([id, datasource]) => {
-          indexPatterns.push(
-            ...datasource.getMetaData(state.datasourceStates[id].state).filterableIndexPatterns
-          );
-        });
-
-      const doc = getSavedObjectFormat({
-        activeDatasources: Object.keys(state.datasourceStates).reduce(
-          (datasourceMap, datasourceId) => ({
-            ...datasourceMap,
-            [datasourceId]: props.datasourceMap[datasourceId],
-          }),
-          {}
-        ),
-        visualization: activeVisualization,
-        state,
-        framePublicAPI,
-      });
-
-      props.onChange({ filterableIndexPatterns: indexPatterns, doc });
+      );
     },
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/expression_helpers.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/expression_helpers.ts
index ee28ccfe1bf53..952718e13c8cf 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/expression_helpers.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/expression_helpers.ts
@@ -5,8 +5,7 @@
  */
 
 import { Ast, fromExpression, ExpressionFunctionAST } from '@kbn/interpreter/common';
-import { Visualization, Datasource, FramePublicAPI } from '../../types';
-import { Filter, TimeRange, Query } from '../../../../../../src/plugins/data/public';
+import { Visualization, Datasource, DatasourcePublicAPI } from '../../types';
 
 export function prependDatasourceExpression(
   visualizationExpression: Ast | string | null,
@@ -58,40 +57,12 @@ export function prependDatasourceExpression(
       ? fromExpression(visualizationExpression)
       : visualizationExpression;
 
-  return {
-    type: 'expression',
-    chain: [datafetchExpression, ...parsedVisualizationExpression.chain],
-  };
-}
-
-export function prependKibanaContext(
-  expression: Ast | string,
-  {
-    timeRange,
-    query,
-    filters,
-  }: {
-    timeRange?: TimeRange;
-    query?: Query;
-    filters?: Filter[];
-  }
-): Ast {
-  const parsedExpression = typeof expression === 'string' ? fromExpression(expression) : expression;
-
   return {
     type: 'expression',
     chain: [
       { type: 'function', function: 'kibana', arguments: {} },
-      {
-        type: 'function',
-        function: 'kibana_context',
-        arguments: {
-          timeRange: timeRange ? [JSON.stringify(timeRange)] : [],
-          query: query ? [JSON.stringify(query)] : [],
-          filters: [JSON.stringify(filters || [])],
-        },
-      },
-      ...parsedExpression.chain,
+      datafetchExpression,
+      ...parsedVisualizationExpression.chain,
     ],
   };
 }
@@ -101,8 +72,7 @@ export function buildExpression({
   visualizationState,
   datasourceMap,
   datasourceStates,
-  framePublicAPI,
-  removeDateRange,
+  datasourceLayers,
 }: {
   visualization: Visualization | null;
   visualizationState: unknown;
@@ -114,24 +84,12 @@ export function buildExpression({
       state: unknown;
     }
   >;
-  framePublicAPI: FramePublicAPI;
-  removeDateRange?: boolean;
+  datasourceLayers: Record<string, DatasourcePublicAPI>;
 }): Ast | null {
   if (visualization === null) {
     return null;
   }
-  const visualizationExpression = visualization.toExpression(visualizationState, framePublicAPI);
-
-  const expressionContext = removeDateRange
-    ? { query: framePublicAPI.query, filters: framePublicAPI.filters }
-    : {
-        query: framePublicAPI.query,
-        timeRange: {
-          from: framePublicAPI.dateRange.fromDate,
-          to: framePublicAPI.dateRange.toDate,
-        },
-        filters: framePublicAPI.filters,
-      };
+  const visualizationExpression = visualization.toExpression(visualizationState, datasourceLayers);
 
   const completeExpression = prependDatasourceExpression(
     visualizationExpression,
@@ -139,9 +97,5 @@ export function buildExpression({
     datasourceStates
   );
 
-  if (completeExpression) {
-    return prependKibanaContext(completeExpression, expressionContext);
-  } else {
-    return null;
-  }
+  return completeExpression;
 }
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.test.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.test.ts
index d72e5c57ce56e..45d24fd30e2fc 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.test.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.test.ts
@@ -8,14 +8,18 @@ import { getSavedObjectFormat, Props } from './save';
 import { createMockDatasource, createMockVisualization } from '../mocks';
 import { esFilters, IIndexPattern, IFieldType } from '../../../../../../src/plugins/data/public';
 
+jest.mock('./expression_helpers');
+
 describe('save editor frame state', () => {
   const mockVisualization = createMockVisualization();
-  mockVisualization.getPersistableState.mockImplementation((x) => x);
   const mockDatasource = createMockDatasource('a');
   const mockIndexPattern = ({ id: 'indexpattern' } as unknown) as IIndexPattern;
   const mockField = ({ name: '@timestamp' } as unknown) as IFieldType;
 
-  mockDatasource.getPersistableState.mockImplementation((x) => x);
+  mockDatasource.getPersistableState.mockImplementation((x) => ({
+    state: x,
+    savedObjectReferences: [],
+  }));
   const saveArgs: Props = {
     activeDatasources: {
       indexpattern: mockDatasource,
@@ -47,15 +51,17 @@ describe('save editor frame state', () => {
   it('transforms from internal state to persisted doc format', async () => {
     const datasource = createMockDatasource('a');
     datasource.getPersistableState.mockImplementation((state) => ({
-      stuff: `${state}_datasource_persisted`,
+      state: {
+        stuff: `${state}_datasource_persisted`,
+      },
+      savedObjectReferences: [],
     }));
+    datasource.toExpression.mockReturnValue('my | expr');
 
     const visualization = createMockVisualization();
-    visualization.getPersistableState.mockImplementation((state) => ({
-      things: `${state}_vis_persisted`,
-    }));
+    visualization.toExpression.mockReturnValue('vis | expr');
 
-    const doc = await getSavedObjectFormat({
+    const { doc, filterableIndexPatterns, isSaveable } = await getSavedObjectFormat({
       ...saveArgs,
       activeDatasources: {
         indexpattern: datasource,
@@ -74,27 +80,32 @@ describe('save editor frame state', () => {
       visualization,
     });
 
+    expect(filterableIndexPatterns).toEqual([]);
+    expect(isSaveable).toEqual(true);
     expect(doc).toEqual({
       id: undefined,
-      expression: '',
       state: {
-        datasourceMetaData: {
-          filterableIndexPatterns: [],
-        },
         datasourceStates: {
           indexpattern: {
             stuff: '2_datasource_persisted',
           },
         },
-        visualization: { things: '4_vis_persisted' },
+        visualization: '4',
         query: { query: '', language: 'lucene' },
         filters: [
           {
-            meta: { index: 'indexpattern' },
+            meta: { indexRefName: 'filter-index-pattern-0' },
             exists: { field: '@timestamp' },
           },
         ],
       },
+      references: [
+        {
+          id: 'indexpattern',
+          name: 'filter-index-pattern-0',
+          type: 'index-pattern',
+        },
+      ],
       title: 'bbb',
       type: 'lens',
       visualizationType: '3',
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.ts
index b41e93def966e..6da6d5a8c118f 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/save.ts
@@ -5,11 +5,12 @@
  */
 
 import _ from 'lodash';
-import { toExpression } from '@kbn/interpreter/target/common';
+import { SavedObjectReference } from 'kibana/public';
 import { EditorFrameState } from './state_management';
 import { Document } from '../../persistence/saved_object_store';
-import { buildExpression } from './expression_helpers';
 import { Datasource, Visualization, FramePublicAPI } from '../../types';
+import { extractFilterReferences } from '../../persistence';
+import { buildExpression } from './expression_helpers';
 
 export interface Props {
   activeDatasources: Record<string, Datasource>;
@@ -23,43 +24,55 @@ export function getSavedObjectFormat({
   state,
   visualization,
   framePublicAPI,
-}: Props): Document {
+}: Props): {
+  doc: Document;
+  filterableIndexPatterns: string[];
+  isSaveable: boolean;
+} {
+  const datasourceStates: Record<string, unknown> = {};
+  const references: SavedObjectReference[] = [];
+  Object.entries(activeDatasources).forEach(([id, datasource]) => {
+    const { state: persistableState, savedObjectReferences } = datasource.getPersistableState(
+      state.datasourceStates[id].state
+    );
+    datasourceStates[id] = persistableState;
+    references.push(...savedObjectReferences);
+  });
+
+  const uniqueFilterableIndexPatternIds = _.uniq(
+    references.filter(({ type }) => type === 'index-pattern').map(({ id }) => id)
+  );
+
+  const { persistableFilters, references: filterReferences } = extractFilterReferences(
+    framePublicAPI.filters
+  );
+
+  references.push(...filterReferences);
+
   const expression = buildExpression({
     visualization,
     visualizationState: state.visualization.state,
     datasourceMap: activeDatasources,
     datasourceStates: state.datasourceStates,
-    framePublicAPI,
-    removeDateRange: true,
-  });
-
-  const datasourceStates: Record<string, unknown> = {};
-  Object.entries(activeDatasources).forEach(([id, datasource]) => {
-    datasourceStates[id] = datasource.getPersistableState(state.datasourceStates[id].state);
-  });
-
-  const filterableIndexPatterns: Array<{ id: string; title: string }> = [];
-  Object.entries(activeDatasources).forEach(([id, datasource]) => {
-    filterableIndexPatterns.push(
-      ...datasource.getMetaData(state.datasourceStates[id].state).filterableIndexPatterns
-    );
+    datasourceLayers: framePublicAPI.datasourceLayers,
   });
 
   return {
-    id: state.persistedId,
-    title: state.title,
-    description: state.description,
-    type: 'lens',
-    visualizationType: state.visualization.activeId,
-    expression: expression ? toExpression(expression) : '',
-    state: {
-      datasourceStates,
-      datasourceMetaData: {
-        filterableIndexPatterns: _.uniqBy(filterableIndexPatterns, 'id'),
+    doc: {
+      id: state.persistedId,
+      title: state.title,
+      description: state.description,
+      type: 'lens',
+      visualizationType: state.visualization.activeId,
+      state: {
+        datasourceStates,
+        visualization: state.visualization.state,
+        query: framePublicAPI.query,
+        filters: persistableFilters,
       },
-      visualization: visualization.getPersistableState(state.visualization.state),
-      query: framePublicAPI.query,
-      filters: framePublicAPI.filters,
+      references,
     },
+    filterableIndexPatterns: uniqueFilterableIndexPatternIds,
+    isSaveable: expression !== null,
   };
 }
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_helpers.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_helpers.ts
new file mode 100644
index 0000000000000..6deb9ffd37a06
--- /dev/null
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_helpers.ts
@@ -0,0 +1,87 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License;
+ * you may not use this file except in compliance with the Elastic License.
+ */
+
+import { SavedObjectReference } from 'kibana/public';
+import { Ast } from '@kbn/interpreter/common';
+import { Datasource, DatasourcePublicAPI, Visualization } from '../../types';
+import { buildExpression } from './expression_helpers';
+import { Document } from '../../persistence/saved_object_store';
+
+export async function initializeDatasources(
+  datasourceMap: Record<string, Datasource>,
+  datasourceStates: Record<string, { state: unknown; isLoading: boolean }>,
+  references?: SavedObjectReference[]
+) {
+  const states: Record<string, { isLoading: boolean; state: unknown }> = {};
+  await Promise.all(
+    Object.entries(datasourceMap).map(([datasourceId, datasource]) => {
+      if (datasourceStates[datasourceId]) {
+        return datasource
+          .initialize(datasourceStates[datasourceId].state || undefined, references)
+          .then((datasourceState) => {
+            states[datasourceId] = { isLoading: false, state: datasourceState };
+          });
+      }
+    })
+  );
+  return states;
+}
+
+export function createDatasourceLayers(
+  datasourceMap: Record<string, Datasource>,
+  datasourceStates: Record<string, { state: unknown; isLoading: boolean }>
+) {
+  const datasourceLayers: Record<string, DatasourcePublicAPI> = {};
+  Object.keys(datasourceMap)
+    .filter((id) => datasourceStates[id] && !datasourceStates[id].isLoading)
+    .forEach((id) => {
+      const datasourceState = datasourceStates[id].state;
+      const datasource = datasourceMap[id];
+
+      const layers = datasource.getLayers(datasourceState);
+      layers.forEach((layer) => {
+        datasourceLayers[layer] = datasourceMap[id].getPublicAPI({
+          state: datasourceState,
+          layerId: layer,
+        });
+      });
+    });
+  return datasourceLayers;
+}
+
+export async function persistedStateToExpression(
+  datasources: Record<string, Datasource>,
+  visualizations: Record<string, Visualization>,
+  doc: Document
+): Promise<Ast | null> {
+  const {
+    state: { visualization: visualizationState, datasourceStates: persistedDatasourceStates },
+    visualizationType,
+    references,
+  } = doc;
+  if (!visualizationType) return null;
+  const visualization = visualizations[visualizationType!];
+  const datasourceStates = await initializeDatasources(
+    datasources,
+    Object.fromEntries(
+      Object.entries(persistedDatasourceStates).map(([id, state]) => [
+        id,
+        { isLoading: false, state },
+      ])
+    ),
+    references
+  );
+
+  const datasourceLayers = createDatasourceLayers(datasources, datasourceStates);
+
+  return buildExpression({
+    visualization,
+    visualizationState,
+    datasourceMap: datasources,
+    datasourceStates,
+    datasourceLayers,
+  });
+}
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_management.test.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_management.test.ts
index 969467b5789ec..c7f505aeca517 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_management.test.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/state_management.test.ts
@@ -57,19 +57,16 @@ describe('editor_frame state management', () => {
       const initialState = getInitialState({
         ...props,
         doc: {
-          expression: '',
           state: {
             datasourceStates: {
               testDatasource: { internalState1: '' },
               testDatasource2: { internalState2: '' },
             },
             visualization: {},
-            datasourceMetaData: {
-              filterableIndexPatterns: [],
-            },
             query: { query: '', language: 'lucene' },
             filters: [],
           },
+          references: [],
           title: '',
           visualizationType: 'testVis',
         },
@@ -380,9 +377,7 @@ describe('editor_frame state management', () => {
           type: 'VISUALIZATION_LOADED',
           doc: {
             id: 'b',
-            expression: '',
             state: {
-              datasourceMetaData: { filterableIndexPatterns: [] },
               datasourceStates: { a: { foo: 'c' } },
               visualization: { bar: 'd' },
               query: { query: '', language: 'lucene' },
@@ -392,6 +387,7 @@ describe('editor_frame state management', () => {
             description: 'My lens',
             type: 'lens',
             visualizationType: 'line',
+            references: [],
           },
         }
       );
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_helpers.ts b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_helpers.ts
index 263f7cd65f43d..2bb1baf9d54f2 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_helpers.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_helpers.ts
@@ -107,7 +107,7 @@ export function getSuggestions({
  * title and preview expression.
  */
 function getVisualizationSuggestions(
-  visualization: Visualization<unknown, unknown>,
+  visualization: Visualization<unknown>,
   table: TableSuggestion,
   visualizationId: string,
   datasourceSuggestion: DatasourceSuggestion & { datasourceId: string },
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.test.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.test.tsx
index fd509c0046e13..323472d717352 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.test.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.test.tsx
@@ -249,7 +249,6 @@ describe('suggestion_panel', () => {
 
     expect(passedExpression).toMatchInlineSnapshot(`
       "kibana
-      | kibana_context timeRange=\\"{\\\\\\"from\\\\\\":\\\\\\"now-7d\\\\\\",\\\\\\"to\\\\\\":\\\\\\"now\\\\\\"}\\" query=\\"{\\\\\\"query\\\\\\":\\\\\\"\\\\\\",\\\\\\"language\\\\\\":\\\\\\"lucene\\\\\\"}\\" filters=\\"[{\\\\\\"meta\\\\\\":{\\\\\\"index\\\\\\":\\\\\\"index1\\\\\\"},\\\\\\"exists\\\\\\":{\\\\\\"field\\\\\\":\\\\\\"myfield\\\\\\"}}]\\"
       | lens_merge_tables layerIds=\\"first\\" tables={datasource_expression}
       | test
       | expression"
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.tsx
index 7395075cf9f74..f1dc3fa306d15 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/suggestion_panel.tsx
@@ -21,6 +21,7 @@ import { IconType } from '@elastic/eui/src/components/icon/icon';
 import { Ast, toExpression } from '@kbn/interpreter/common';
 import { i18n } from '@kbn/i18n';
 import classNames from 'classnames';
+import { ExecutionContextSearch } from 'src/plugins/expressions';
 import { Action, PreviewState } from './state_management';
 import { Datasource, Visualization, FramePublicAPI, DatasourcePublicAPI } from '../../types';
 import { getSuggestions, switchToSuggestion } from './suggestion_helpers';
@@ -28,7 +29,7 @@ import {
   ReactExpressionRendererProps,
   ReactExpressionRendererType,
 } from '../../../../../../src/plugins/expressions/public';
-import { prependDatasourceExpression, prependKibanaContext } from './expression_helpers';
+import { prependDatasourceExpression } from './expression_helpers';
 import { debouncedComponent } from '../../debounced_component';
 import { trackUiEvent, trackSuggestionEvent } from '../../lens_ui_telemetry';
 import { DataPublicPluginStart } from '../../../../../../src/plugins/data/public';
@@ -112,7 +113,7 @@ const SuggestionPreview = ({
 }: {
   onSelect: () => void;
   preview: {
-    expression?: Ast;
+    expression?: Ast | null;
     icon: IconType;
     title: string;
   };
@@ -215,12 +216,24 @@ export function SuggestionPanel({
     visualizationMap,
   ]);
 
+  const context: ExecutionContextSearch = useMemo(
+    () => ({
+      query: frame.query,
+      timeRange: {
+        from: frame.dateRange.fromDate,
+        to: frame.dateRange.toDate,
+      },
+      filters: frame.filters,
+    }),
+    [frame.query, frame.dateRange.fromDate, frame.dateRange.toDate, frame.filters]
+  );
+
   const AutoRefreshExpressionRenderer = useMemo(() => {
     const autoRefreshFetch$ = plugins.data.query.timefilter.timefilter.getAutoRefreshFetch$();
     return (props: ReactExpressionRendererProps) => (
-      <ExpressionRendererComponent {...props} reload$={autoRefreshFetch$} />
+      <ExpressionRendererComponent {...props} searchContext={context} reload$={autoRefreshFetch$} />
     );
-  }, [plugins.data.query.timefilter.timefilter]);
+  }, [plugins.data.query.timefilter.timefilter, context]);
 
   const [lastSelectedSuggestion, setLastSelectedSuggestion] = useState<number>(-1);
 
@@ -252,15 +265,6 @@ export function SuggestionPanel({
     }
   }
 
-  const expressionContext = {
-    query: frame.query,
-    filters: frame.filters,
-    timeRange: {
-      from: frame.dateRange.fromDate,
-      to: frame.dateRange.toDate,
-    },
-  };
-
   return (
     <div className="lnsSuggestionPanel">
       <EuiFlexGroup alignItems="center">
@@ -305,9 +309,7 @@ export function SuggestionPanel({
         {currentVisualizationId && (
           <SuggestionPreview
             preview={{
-              expression: currentStateExpression
-                ? prependKibanaContext(currentStateExpression, expressionContext)
-                : undefined,
+              expression: currentStateExpression,
               icon:
                 visualizationMap[currentVisualizationId].getDescription(currentVisualizationState)
                   .icon || 'empty',
@@ -325,9 +327,7 @@ export function SuggestionPanel({
           return (
             <SuggestionPreview
               preview={{
-                expression: suggestion.previewExpression
-                  ? prependKibanaContext(suggestion.previewExpression, expressionContext)
-                  : undefined,
+                expression: suggestion.previewExpression,
                 icon: suggestion.previewIcon,
                 title: suggestion.title,
               }}
@@ -391,7 +391,6 @@ function getPreviewExpression(
       if (updatedLayerApis[layerId]) {
         updatedLayerApis[layerId] = datasource.getPublicAPI({
           layerId,
-          dateRange: frame.dateRange,
           state: datasourceState,
         });
       }
@@ -400,7 +399,7 @@ function getPreviewExpression(
 
   return visualization.toPreviewExpression(
     visualizableState.visualizationState,
-    suggestionFrameApi
+    suggestionFrameApi.datasourceLayers
   );
 }
 
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/chart_switch.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/chart_switch.tsx
index 88b791a7875ef..5640c52ac4325 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/chart_switch.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/chart_switch.tsx
@@ -260,7 +260,7 @@ export function ChartSwitch(props: Props) {
 function getTopSuggestion(
   props: Props,
   visualizationId: string,
-  newVisualization: Visualization<unknown, unknown>,
+  newVisualization: Visualization<unknown>,
   subVisualizationId?: string
 ): Suggestion | undefined {
   const unfilteredSuggestions = getSuggestions({
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.test.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.test.tsx
index a9c638df8cad1..47e3b41df3b21 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.test.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.test.tsx
@@ -172,21 +172,6 @@ describe('workspace_panel', () => {
             "function": "kibana",
             "type": "function",
           },
-          Object {
-            "arguments": Object {
-              "filters": Array [
-                "[]",
-              ],
-              "query": Array [
-                "{\\"query\\":\\"\\",\\"language\\":\\"lucene\\"}",
-              ],
-              "timeRange": Array [
-                "{\\"from\\":\\"now-7d\\",\\"to\\":\\"now\\"}",
-              ],
-            },
-            "function": "kibana_context",
-            "type": "function",
-          },
           Object {
             "arguments": Object {
               "layerIds": Array [
@@ -305,10 +290,10 @@ describe('workspace_panel', () => {
     );
 
     expect(
-      (instance.find(expressionRendererMock).prop('expression') as Ast).chain[2].arguments.layerIds
+      (instance.find(expressionRendererMock).prop('expression') as Ast).chain[1].arguments.layerIds
     ).toEqual(['first', 'second', 'third']);
     expect(
-      (instance.find(expressionRendererMock).prop('expression') as Ast).chain[2].arguments.tables
+      (instance.find(expressionRendererMock).prop('expression') as Ast).chain[1].arguments.tables
     ).toMatchInlineSnapshot(`
                                     Array [
                                       Object {
diff --git a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.tsx b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.tsx
index b3a12271f377b..4f914bc65dc7c 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/editor_frame/workspace_panel/workspace_panel.tsx
@@ -18,6 +18,7 @@ import {
   EuiLink,
 } from '@elastic/eui';
 import { CoreStart, CoreSetup } from 'kibana/public';
+import { ExecutionContextSearch } from 'src/plugins/expressions';
 import {
   ExpressionRendererEvent,
   ReactExpressionRendererType,
@@ -129,7 +130,7 @@ export function InnerWorkspacePanel({
           visualizationState,
           datasourceMap,
           datasourceStates,
-          framePublicAPI,
+          datasourceLayers: framePublicAPI.datasourceLayers,
         });
       } catch (e) {
         // Most likely an error in the expression provided by a datasource or visualization
@@ -173,6 +174,23 @@ export function InnerWorkspacePanel({
     [plugins.data.query.timefilter.timefilter]
   );
 
+  const context: ExecutionContextSearch = useMemo(
+    () => ({
+      query: framePublicAPI.query,
+      timeRange: {
+        from: framePublicAPI.dateRange.fromDate,
+        to: framePublicAPI.dateRange.toDate,
+      },
+      filters: framePublicAPI.filters,
+    }),
+    [
+      framePublicAPI.query,
+      framePublicAPI.dateRange.fromDate,
+      framePublicAPI.dateRange.toDate,
+      framePublicAPI.filters,
+    ]
+  );
+
   useEffect(() => {
     // reset expression error if component attempts to run it again
     if (expression && localState.expressionBuildError) {
@@ -264,6 +282,7 @@ export function InnerWorkspacePanel({
           className="lnsExpressionRenderer__component"
           padding="m"
           expression={expression!}
+          searchContext={context}
           reload$={autoRefreshFetch$}
           onEvent={onEvent}
           renderError={(errorMessage?: string | null) => {
diff --git a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.test.tsx b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.test.tsx
index 69447b3b9a9b8..1e2df28cad7b1 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.test.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.test.tsx
@@ -18,16 +18,13 @@ jest.mock('../../../../../../src/plugins/inspector/public/', () => ({
 }));
 
 const savedVis: Document = {
-  expression: 'my | expression',
   state: {
     visualization: {},
     datasourceStates: {},
-    datasourceMetaData: {
-      filterableIndexPatterns: [],
-    },
     query: { query: '', language: 'lucene' },
     filters: [],
   },
+  references: [],
   title: 'My title',
   visualizationType: '',
 };
@@ -59,13 +56,14 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123' }
     );
     embeddable.render(mountpoint);
 
     expect(expressionRenderer).toHaveBeenCalledTimes(1);
-    expect(expressionRenderer.mock.calls[0][0]!.expression).toEqual(savedVis.expression);
+    expect(expressionRenderer.mock.calls[0][0]!.expression).toEqual('my | expression');
   });
 
   it('should re-render if new input is pushed', () => {
@@ -82,6 +80,7 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123' }
     );
@@ -110,6 +109,7 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123', timeRange, query, filters }
     );
@@ -117,11 +117,52 @@ describe('embeddable', () => {
 
     expect(expressionRenderer.mock.calls[0][0].searchContext).toEqual({
       timeRange,
-      query,
+      query: [query, savedVis.state.query],
       filters,
     });
   });
 
+  it('should merge external context with query and filters of the saved object', () => {
+    const timeRange: TimeRange = { from: 'now-15d', to: 'now' };
+    const query: Query = { language: 'kquery', query: 'external filter' };
+    const filters: Filter[] = [{ meta: { alias: 'test', negate: false, disabled: false } }];
+
+    const embeddable = new Embeddable(
+      dataPluginMock.createSetupContract().query.timefilter.timefilter,
+      expressionRenderer,
+      getTrigger,
+      {
+        editPath: '',
+        editUrl: '',
+        editable: true,
+        savedVis: {
+          ...savedVis,
+          state: {
+            ...savedVis.state,
+            query: { language: 'kquery', query: 'saved filter' },
+            filters: [
+              { meta: { alias: 'test', negate: false, disabled: false, indexRefName: 'filter-0' } },
+            ],
+          },
+          references: [{ type: 'index-pattern', name: 'filter-0', id: 'my-index-pattern-id' }],
+        },
+        expression: 'my | expression',
+      },
+      { id: '123', timeRange, query, filters }
+    );
+    embeddable.render(mountpoint);
+
+    expect(expressionRenderer.mock.calls[0][0].searchContext).toEqual({
+      timeRange,
+      query: [query, { language: 'kquery', query: 'saved filter' }],
+      filters: [
+        filters[0],
+        // actual index pattern id gets injected
+        { meta: { alias: 'test', negate: false, disabled: false, index: 'my-index-pattern-id' } },
+      ],
+    });
+  });
+
   it('should execute trigger on event from expression renderer', () => {
     const embeddable = new Embeddable(
       dataPluginMock.createSetupContract().query.timefilter.timefilter,
@@ -132,6 +173,7 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123' }
     );
@@ -162,6 +204,7 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123', timeRange, query, filters }
     );
@@ -195,6 +238,7 @@ describe('embeddable', () => {
         editUrl: '',
         editable: true,
         savedVis,
+        expression: 'my | expression',
       },
       { id: '123', timeRange, query, filters }
     );
diff --git a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.tsx b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.tsx
index bbd2b18907e9b..4df218a3e94e9 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable.tsx
@@ -14,6 +14,7 @@ import {
   TimefilterContract,
   TimeRange,
 } from 'src/plugins/data/public';
+import { ExecutionContextSearch } from 'src/plugins/expressions';
 
 import { Subscription } from 'rxjs';
 import {
@@ -28,12 +29,13 @@ import {
   EmbeddableOutput,
   IContainer,
 } from '../../../../../../src/plugins/embeddable/public';
-import { DOC_TYPE, Document } from '../../persistence';
+import { DOC_TYPE, Document, injectFilterReferences } from '../../persistence';
 import { ExpressionWrapper } from './expression_wrapper';
 import { UiActionsStart } from '../../../../../../src/plugins/ui_actions/public';
 import { isLensBrushEvent, isLensFilterEvent } from '../../types';
 
 export interface LensEmbeddableConfiguration {
+  expression: string | null;
   savedVis: Document;
   editUrl: string;
   editPath: string;
@@ -56,12 +58,13 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
 
   private expressionRenderer: ReactExpressionRendererType;
   private getTrigger: UiActionsStart['getTrigger'] | undefined;
+  private expression: string | null;
   private savedVis: Document;
   private domNode: HTMLElement | Element | undefined;
   private subscription: Subscription;
   private autoRefreshFetchSubscription: Subscription;
 
-  private currentContext: {
+  private externalSearchContext: {
     timeRange?: TimeRange;
     query?: Query;
     filters?: Filter[];
@@ -72,7 +75,14 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
     timefilter: TimefilterContract,
     expressionRenderer: ReactExpressionRendererType,
     getTrigger: UiActionsStart['getTrigger'] | undefined,
-    { savedVis, editPath, editUrl, editable, indexPatterns }: LensEmbeddableConfiguration,
+    {
+      expression,
+      savedVis,
+      editPath,
+      editUrl,
+      editable,
+      indexPatterns,
+    }: LensEmbeddableConfiguration,
     initialInput: LensEmbeddableInput,
     parent?: IContainer
   ) {
@@ -95,6 +105,7 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
 
     this.getTrigger = getTrigger;
     this.expressionRenderer = expressionRenderer;
+    this.expression = expression;
     this.savedVis = savedVis;
     this.subscription = this.getInput$().subscribe((input) => this.onContainerStateChanged(input));
     this.onContainerStateChanged(initialInput);
@@ -122,14 +133,14 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
       ? containerState.filters.filter((filter) => !filter.meta.disabled)
       : undefined;
     if (
-      !_.isEqual(containerState.timeRange, this.currentContext.timeRange) ||
-      !_.isEqual(containerState.query, this.currentContext.query) ||
-      !_.isEqual(cleanedFilters, this.currentContext.filters)
+      !_.isEqual(containerState.timeRange, this.externalSearchContext.timeRange) ||
+      !_.isEqual(containerState.query, this.externalSearchContext.query) ||
+      !_.isEqual(cleanedFilters, this.externalSearchContext.filters)
     ) {
-      this.currentContext = {
+      this.externalSearchContext = {
         timeRange: containerState.timeRange,
         query: containerState.query,
-        lastReloadRequestTime: this.currentContext.lastReloadRequestTime,
+        lastReloadRequestTime: this.externalSearchContext.lastReloadRequestTime,
         filters: cleanedFilters,
       };
 
@@ -149,14 +160,37 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
     render(
       <ExpressionWrapper
         ExpressionRenderer={this.expressionRenderer}
-        expression={this.savedVis.expression}
-        context={this.currentContext}
+        expression={this.expression}
+        searchContext={this.getMergedSearchContext()}
         handleEvent={this.handleEvent}
       />,
       domNode
     );
   }
 
+  /**
+   * Combines the embeddable context with the saved object context, and replaces
+   * any references to index patterns
+   */
+  private getMergedSearchContext(): ExecutionContextSearch {
+    const output: ExecutionContextSearch = {
+      timeRange: this.externalSearchContext.timeRange,
+    };
+    if (this.externalSearchContext.query) {
+      output.query = [this.externalSearchContext.query, this.savedVis.state.query];
+    } else {
+      output.query = [this.savedVis.state.query];
+    }
+    if (this.externalSearchContext.filters?.length) {
+      output.filters = [...this.externalSearchContext.filters, ...this.savedVis.state.filters];
+    } else {
+      output.filters = [...this.savedVis.state.filters];
+    }
+
+    output.filters = injectFilterReferences(output.filters, this.savedVis.references);
+    return output;
+  }
+
   handleEvent = (event: ExpressionRendererEvent) => {
     if (!this.getTrigger || this.input.disableTriggers) {
       return;
@@ -188,9 +222,9 @@ export class Embeddable extends AbstractEmbeddable<LensEmbeddableInput, LensEmbe
 
   reload() {
     const currentTime = Date.now();
-    if (this.currentContext.lastReloadRequestTime !== currentTime) {
-      this.currentContext = {
-        ...this.currentContext,
+    if (this.externalSearchContext.lastReloadRequestTime !== currentTime) {
+      this.externalSearchContext = {
+        ...this.externalSearchContext,
         lastReloadRequestTime: currentTime,
       };
 
diff --git a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable_factory.ts b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable_factory.ts
index 9a901d3631ec3..b8f9f8de1d286 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable_factory.ts
+++ b/x-pack/plugins/lens/public/editor_frame_service/embeddable/embeddable_factory.ts
@@ -7,6 +7,7 @@
 import { Capabilities, HttpSetup, SavedObjectsClientContract } from 'kibana/public';
 import { i18n } from '@kbn/i18n';
 import { RecursiveReadonly } from '@kbn/utility-types';
+import { toExpression, Ast } from '@kbn/interpreter/target/common';
 import {
   IndexPatternsContract,
   IndexPattern,
@@ -23,6 +24,7 @@ import { Embeddable } from './embeddable';
 import { SavedObjectIndexStore, DOC_TYPE } from '../../persistence';
 import { getEditPath } from '../../../common';
 import { UiActionsStart } from '../../../../../../src/plugins/ui_actions/public';
+import { Document } from '../../persistence/saved_object_store';
 
 interface StartServices {
   timefilter: TimefilterContract;
@@ -32,6 +34,7 @@ interface StartServices {
   expressionRenderer: ReactExpressionRendererType;
   indexPatternService: IndexPatternsContract;
   uiActions?: UiActionsStart;
+  documentToExpression: (doc: Document) => Promise<Ast | null>;
 }
 
 export class EmbeddableFactory implements EmbeddableFactoryDefinition {
@@ -72,13 +75,15 @@ export class EmbeddableFactory implements EmbeddableFactoryDefinition {
       indexPatternService,
       timefilter,
       expressionRenderer,
+      documentToExpression,
       uiActions,
     } = await this.getStartServices();
     const store = new SavedObjectIndexStore(savedObjectsClient);
     const savedVis = await store.load(savedObjectId);
 
-    const promises = savedVis.state.datasourceMetaData.filterableIndexPatterns.map(
-      async ({ id }) => {
+    const promises = savedVis.references
+      .filter(({ type }) => type === 'index-pattern')
+      .map(async ({ id }) => {
         try {
           return await indexPatternService.get(id);
         } catch (error) {
@@ -87,14 +92,15 @@ export class EmbeddableFactory implements EmbeddableFactoryDefinition {
           // to show.
           return null;
         }
-      }
-    );
+      });
     const indexPatterns = (
       await Promise.all(promises)
     ).filter((indexPattern: IndexPattern | null): indexPattern is IndexPattern =>
       Boolean(indexPattern)
     );
 
+    const expression = await documentToExpression(savedVis);
+
     return new Embeddable(
       timefilter,
       expressionRenderer,
@@ -105,6 +111,7 @@ export class EmbeddableFactory implements EmbeddableFactoryDefinition {
         editUrl: coreHttp.basePath.prepend(`/app/lens${getEditPath(savedObjectId)}`),
         editable: await this.isEditable(),
         indexPatterns,
+        expression: expression ? toExpression(expression) : null,
       },
       input,
       parent
diff --git a/x-pack/plugins/lens/public/editor_frame_service/embeddable/expression_wrapper.tsx b/x-pack/plugins/lens/public/editor_frame_service/embeddable/expression_wrapper.tsx
index 296dcef3e70b9..d0d2360ddc107 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/embeddable/expression_wrapper.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/embeddable/expression_wrapper.tsx
@@ -8,28 +8,23 @@ import React from 'react';
 import { I18nProvider } from '@kbn/i18n/react';
 import { FormattedMessage } from '@kbn/i18n/react';
 import { EuiFlexGroup, EuiFlexItem, EuiText, EuiIcon } from '@elastic/eui';
-import { TimeRange, Filter, Query } from 'src/plugins/data/public';
 import {
   ExpressionRendererEvent,
   ReactExpressionRendererType,
 } from 'src/plugins/expressions/public';
+import { ExecutionContextSearch } from 'src/plugins/expressions';
 
 export interface ExpressionWrapperProps {
   ExpressionRenderer: ReactExpressionRendererType;
   expression: string | null;
-  context: {
-    timeRange?: TimeRange;
-    query?: Query;
-    filters?: Filter[];
-    lastReloadRequestTime?: number;
-  };
+  searchContext: ExecutionContextSearch;
   handleEvent: (event: ExpressionRendererEvent) => void;
 }
 
 export function ExpressionWrapper({
   ExpressionRenderer: ExpressionRendererComponent,
   expression,
-  context,
+  searchContext,
   handleEvent,
 }: ExpressionWrapperProps) {
   return (
@@ -54,7 +49,7 @@ export function ExpressionWrapper({
             className="lnsExpressionRenderer__component"
             padding="m"
             expression={expression}
-            searchContext={{ ...context }}
+            searchContext={searchContext}
             renderError={(error) => <div data-test-subj="expression-renderer-error">{error}</div>}
             onEvent={handleEvent}
           />
diff --git a/x-pack/plugins/lens/public/editor_frame_service/mocks.tsx b/x-pack/plugins/lens/public/editor_frame_service/mocks.tsx
index 9c0825b3c2d27..86b137851d9bd 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/mocks.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/mocks.tsx
@@ -31,7 +31,6 @@ export function createMockVisualization(): jest.Mocked<Visualization> {
     getVisualizationTypeId: jest.fn((_state) => 'empty'),
     getDescription: jest.fn((_state) => ({ label: '' })),
     switchVisualizationType: jest.fn((_, x) => x),
-    getPersistableState: jest.fn((_state) => _state),
     getSuggestions: jest.fn((_options) => []),
     initialize: jest.fn((_frame, _state?) => ({})),
     getConfiguration: jest.fn((props) => ({
@@ -71,7 +70,7 @@ export function createMockDatasource(id: string): DatasourceMock {
     clearLayer: jest.fn((state, _layerId) => state),
     getDatasourceSuggestionsForField: jest.fn((_state, _item) => []),
     getDatasourceSuggestionsFromCurrentState: jest.fn((_state) => []),
-    getPersistableState: jest.fn(),
+    getPersistableState: jest.fn((x) => ({ state: x, savedObjectReferences: [] })),
     getPublicAPI: jest.fn().mockReturnValue(publicAPIMock),
     initialize: jest.fn((_state?) => Promise.resolve()),
     renderDataPanel: jest.fn(),
@@ -81,7 +80,6 @@ export function createMockDatasource(id: string): DatasourceMock {
     removeLayer: jest.fn((_state, _layerId) => {}),
     removeColumn: jest.fn((props) => {}),
     getLayers: jest.fn((_state) => []),
-    getMetaData: jest.fn((_state) => ({ filterableIndexPatterns: [] })),
 
     renderDimensionTrigger: jest.fn(),
     renderDimensionEditor: jest.fn(),
diff --git a/x-pack/plugins/lens/public/editor_frame_service/service.tsx b/x-pack/plugins/lens/public/editor_frame_service/service.tsx
index 47339373b6d1a..5fc347179a032 100644
--- a/x-pack/plugins/lens/public/editor_frame_service/service.tsx
+++ b/x-pack/plugins/lens/public/editor_frame_service/service.tsx
@@ -21,12 +21,14 @@ import {
   EditorFrameInstance,
   EditorFrameStart,
 } from '../types';
+import { Document } from '../persistence/saved_object_store';
 import { EditorFrame } from './editor_frame';
 import { mergeTables } from './merge_tables';
 import { formatColumn } from './format_column';
 import { EmbeddableFactory } from './embeddable/embeddable_factory';
 import { getActiveDatasourceIdFromDoc } from './editor_frame/state_management';
 import { UiActionsStart } from '../../../../../src/plugins/ui_actions/public';
+import { persistedStateToExpression } from './editor_frame/state_helpers';
 
 export interface EditorFrameSetupPlugins {
   data: DataPublicPluginSetup;
@@ -59,6 +61,21 @@ export class EditorFrameService {
   private readonly datasources: Array<Datasource | Promise<Datasource>> = [];
   private readonly visualizations: Array<Visualization | Promise<Visualization>> = [];
 
+  /**
+   * This method takes a Lens saved object as returned from the persistence helper,
+   * initializes datsources and visualization and creates the current expression.
+   * This is an asynchronous process and should only be triggered once for a saved object.
+   * @param doc parsed Lens saved object
+   */
+  private async documentToExpression(doc: Document) {
+    const [resolvedDatasources, resolvedVisualizations] = await Promise.all([
+      collectAsyncDefinitions(this.datasources),
+      collectAsyncDefinitions(this.visualizations),
+    ]);
+
+    return await persistedStateToExpression(resolvedDatasources, resolvedVisualizations, doc);
+  }
+
   public setup(
     core: CoreSetup<EditorFrameStartPlugins>,
     plugins: EditorFrameSetupPlugins
@@ -74,6 +91,7 @@ export class EditorFrameService {
         coreHttp: coreStart.http,
         timefilter: deps.data.query.timefilter.timefilter,
         expressionRenderer: deps.expressions.ReactExpressionRenderer,
+        documentToExpression: this.documentToExpression.bind(this),
         indexPatternService: deps.data.indexPatterns,
         uiActions: deps.uiActions,
       };
@@ -88,7 +106,7 @@ export class EditorFrameService {
         this.datasources.push(datasource as Datasource<unknown, unknown>);
       },
       registerVisualization: (visualization) => {
-        this.visualizations.push(visualization as Visualization<unknown, unknown>);
+        this.visualizations.push(visualization as Visualization<unknown>);
       },
     };
   }
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/__mocks__/loader.ts b/x-pack/plugins/lens/public/indexpattern_datasource/__mocks__/loader.ts
index ca5fe706985f8..c487e31f5a973 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/__mocks__/loader.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/__mocks__/loader.ts
@@ -23,3 +23,7 @@ export function loadInitialState() {
   };
   return result;
 }
+
+const originalLoader = jest.requireActual('../loader');
+
+export const extractReferences = originalLoader.extractReferences;
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.test.ts b/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.test.ts
index dc3938ce436e5..0ba7b7df97853 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.test.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.test.ts
@@ -128,12 +128,15 @@ const expectedIndexPatterns = {
   },
 };
 
-function stateFromPersistedState(
-  persistedState: IndexPatternPersistedState
-): IndexPatternPrivateState {
+type IndexPatternBaseState = Omit<
+  IndexPatternPrivateState,
+  'indexPatternRefs' | 'indexPatterns' | 'existingFields' | 'isFirstExistenceFetch'
+>;
+
+function enrichBaseState(baseState: IndexPatternBaseState): IndexPatternPrivateState {
   return {
-    currentIndexPatternId: persistedState.currentIndexPatternId,
-    layers: persistedState.layers,
+    currentIndexPatternId: baseState.currentIndexPatternId,
+    layers: baseState.layers,
     indexPatterns: expectedIndexPatterns,
     indexPatternRefs: [],
     existingFields: {},
@@ -142,7 +145,10 @@ function stateFromPersistedState(
 }
 
 describe('IndexPattern Data Source', () => {
-  let persistedState: IndexPatternPersistedState;
+  let baseState: Omit<
+    IndexPatternPrivateState,
+    'indexPatternRefs' | 'indexPatterns' | 'existingFields' | 'isFirstExistenceFetch'
+  >;
   let indexPatternDatasource: Datasource<IndexPatternPrivateState, IndexPatternPersistedState>;
 
   beforeEach(() => {
@@ -153,7 +159,7 @@ describe('IndexPattern Data Source', () => {
       charts: chartPluginMock.createSetupContract(),
     });
 
-    persistedState = {
+    baseState = {
       currentIndexPatternId: '1',
       layers: {
         first: {
@@ -224,9 +230,37 @@ describe('IndexPattern Data Source', () => {
 
   describe('#getPersistedState', () => {
     it('should persist from saved state', async () => {
-      const state = stateFromPersistedState(persistedState);
+      const state = enrichBaseState(baseState);
 
-      expect(indexPatternDatasource.getPersistableState(state)).toEqual(persistedState);
+      expect(indexPatternDatasource.getPersistableState(state)).toEqual({
+        state: {
+          layers: {
+            first: {
+              columnOrder: ['col1'],
+              columns: {
+                col1: {
+                  label: 'My Op',
+                  dataType: 'string',
+                  isBucketed: true,
+
+                  // Private
+                  operationType: 'terms',
+                  sourceField: 'op',
+                  params: {
+                    size: 5,
+                    orderBy: { type: 'alphabetical' },
+                    orderDirection: 'asc',
+                  },
+                },
+              },
+            },
+          },
+        },
+        savedObjectReferences: [
+          { name: 'indexpattern-datasource-current-indexpattern', type: 'index-pattern', id: '1' },
+          { name: 'indexpattern-datasource-layer-first', type: 'index-pattern', id: '1' },
+        ],
+      });
     });
   });
 
@@ -237,7 +271,7 @@ describe('IndexPattern Data Source', () => {
     });
 
     it('should generate an expression for an aggregated query', async () => {
-      const queryPersistedState: IndexPatternPersistedState = {
+      const queryBaseState: IndexPatternBaseState = {
         currentIndexPatternId: '1',
         layers: {
           first: {
@@ -266,7 +300,7 @@ describe('IndexPattern Data Source', () => {
         },
       };
 
-      const state = stateFromPersistedState(queryPersistedState);
+      const state = enrichBaseState(queryBaseState);
 
       expect(indexPatternDatasource.toExpression(state, 'first')).toMatchInlineSnapshot(`
         Object {
@@ -311,7 +345,7 @@ describe('IndexPattern Data Source', () => {
     });
 
     it('should put all time fields used in date_histograms to the esaggs timeFields parameter', async () => {
-      const queryPersistedState: IndexPatternPersistedState = {
+      const queryBaseState: IndexPatternBaseState = {
         currentIndexPatternId: '1',
         layers: {
           first: {
@@ -350,14 +384,14 @@ describe('IndexPattern Data Source', () => {
         },
       };
 
-      const state = stateFromPersistedState(queryPersistedState);
+      const state = enrichBaseState(queryBaseState);
 
       const ast = indexPatternDatasource.toExpression(state, 'first') as Ast;
       expect(ast.chain[0].arguments.timeFields).toEqual(['timestamp', 'another_datefield']);
     });
 
     it('should not put date fields used outside date_histograms to the esaggs timeFields parameter', async () => {
-      const queryPersistedState: IndexPatternPersistedState = {
+      const queryBaseState: IndexPatternBaseState = {
         currentIndexPatternId: '1',
         layers: {
           first: {
@@ -386,7 +420,7 @@ describe('IndexPattern Data Source', () => {
         },
       };
 
-      const state = stateFromPersistedState(queryPersistedState);
+      const state = enrichBaseState(queryBaseState);
 
       const ast = indexPatternDatasource.toExpression(state, 'first') as Ast;
       expect(ast.chain[0].arguments.timeFields).toEqual(['timestamp']);
@@ -489,55 +523,14 @@ describe('IndexPattern Data Source', () => {
     });
   });
 
-  describe('#getMetadata', () => {
-    it('should return the title of the index patterns', () => {
-      expect(
-        indexPatternDatasource.getMetaData({
-          indexPatternRefs: [],
-          existingFields: {},
-          isFirstExistenceFetch: false,
-          indexPatterns: expectedIndexPatterns,
-          layers: {
-            first: {
-              indexPatternId: '1',
-              columnOrder: [],
-              columns: {},
-            },
-            second: {
-              indexPatternId: '2',
-              columnOrder: [],
-              columns: {},
-            },
-          },
-          currentIndexPatternId: '1',
-        })
-      ).toEqual({
-        filterableIndexPatterns: [
-          {
-            id: '1',
-            title: 'my-fake-index-pattern',
-          },
-          {
-            id: '2',
-            title: 'my-fake-restricted-pattern',
-          },
-        ],
-      });
-    });
-  });
-
   describe('#getPublicAPI', () => {
     let publicAPI: DatasourcePublicAPI;
 
     beforeEach(async () => {
-      const initialState = stateFromPersistedState(persistedState);
+      const initialState = enrichBaseState(baseState);
       publicAPI = indexPatternDatasource.getPublicAPI({
         state: initialState,
         layerId: 'first',
-        dateRange: {
-          fromDate: 'now-30d',
-          toDate: 'now',
-        },
       });
     });
 
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.tsx b/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.tsx
index 2fb8d7fe0e553..e2ca933504849 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.tsx
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/indexpattern.tsx
@@ -8,7 +8,7 @@ import _ from 'lodash';
 import React from 'react';
 import { render } from 'react-dom';
 import { I18nProvider } from '@kbn/i18n/react';
-import { CoreStart } from 'kibana/public';
+import { CoreStart, SavedObjectReference } from 'kibana/public';
 import { i18n } from '@kbn/i18n';
 import { IStorageWrapper } from 'src/plugins/kibana_utils/public';
 import {
@@ -19,7 +19,12 @@ import {
   DatasourceLayerPanelProps,
   PublicAPIProps,
 } from '../types';
-import { loadInitialState, changeIndexPattern, changeLayerIndexPattern } from './loader';
+import {
+  loadInitialState,
+  changeIndexPattern,
+  changeLayerIndexPattern,
+  extractReferences,
+} from './loader';
 import { toExpression } from './to_expression';
 import {
   IndexPatternDimensionTrigger,
@@ -125,9 +130,13 @@ export function getIndexPatternDatasource({
   const indexPatternDatasource: Datasource<IndexPatternPrivateState, IndexPatternPersistedState> = {
     id: 'indexpattern',
 
-    async initialize(state?: IndexPatternPersistedState) {
+    async initialize(
+      persistedState?: IndexPatternPersistedState,
+      references?: SavedObjectReference[]
+    ) {
       return loadInitialState({
-        state,
+        persistedState,
+        references,
         savedObjectsClient: await savedObjectsClient,
         defaultIndexPatternId: core.uiSettings.get('defaultIndex'),
         storage,
@@ -135,8 +144,8 @@ export function getIndexPatternDatasource({
       });
     },
 
-    getPersistableState({ currentIndexPatternId, layers }: IndexPatternPrivateState) {
-      return { currentIndexPatternId, layers };
+    getPersistableState(state: IndexPatternPrivateState) {
+      return extractReferences(state);
     },
 
     insertLayer(state: IndexPatternPrivateState, newLayerId: string) {
@@ -183,19 +192,6 @@ export function getIndexPatternDatasource({
 
     toExpression,
 
-    getMetaData(state: IndexPatternPrivateState) {
-      return {
-        filterableIndexPatterns: _.uniq(
-          Object.values(state.layers)
-            .map((layer) => layer.indexPatternId)
-            .map((indexPatternId) => ({
-              id: indexPatternId,
-              title: state.indexPatterns[indexPatternId].title,
-            }))
-        ),
-      };
-    },
-
     renderDataPanel(
       domElement: Element,
       props: DatasourceDataPanelProps<IndexPatternPrivateState>
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/loader.test.ts b/x-pack/plugins/lens/public/indexpattern_datasource/loader.test.ts
index cfabcb4edcef7..d80bf779a5d17 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/loader.test.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/loader.test.ts
@@ -12,6 +12,8 @@ import {
   changeIndexPattern,
   changeLayerIndexPattern,
   syncExistingFields,
+  extractReferences,
+  injectReferences,
 } from './loader';
 import { IndexPatternsContract } from '../../../../../src/plugins/data/public';
 import {
@@ -378,10 +380,8 @@ describe('loader', () => {
 
     it('should initialize from saved state', async () => {
       const savedState: IndexPatternPersistedState = {
-        currentIndexPatternId: '2',
         layers: {
           layerb: {
-            indexPatternId: '2',
             columnOrder: ['col1', 'col2'],
             columns: {
               col1: {
@@ -407,7 +407,12 @@ describe('loader', () => {
       };
       const storage = createMockStorage({ indexPatternId: '1' });
       const state = await loadInitialState({
-        state: savedState,
+        persistedState: savedState,
+        references: [
+          { name: 'indexpattern-datasource-current-indexpattern', id: '2', type: 'index-pattern' },
+          { name: 'indexpattern-datasource-layer-layerb', id: '2', type: 'index-pattern' },
+          { name: 'another-reference', id: 'c', type: 'index-pattern' },
+        ],
         savedObjectsClient: mockClient(),
         indexPatternsService: mockIndexPatternsService(),
         storage,
@@ -422,7 +427,7 @@ describe('loader', () => {
         indexPatterns: {
           '2': sampleIndexPatterns['2'],
         },
-        layers: savedState.layers,
+        layers: { layerb: { ...savedState.layers.layerb, indexPatternId: '2' } },
       });
 
       expect(storage.set).toHaveBeenCalledWith('lens-settings', {
@@ -431,6 +436,79 @@ describe('loader', () => {
     });
   });
 
+  describe('saved object references', () => {
+    const state: IndexPatternPrivateState = {
+      currentIndexPatternId: 'b',
+      indexPatternRefs: [],
+      indexPatterns: {},
+      existingFields: {},
+      layers: {
+        a: {
+          indexPatternId: 'id-index-pattern-a',
+          columnOrder: ['col1'],
+          columns: {
+            col1: {
+              dataType: 'number',
+              isBucketed: false,
+              label: '',
+              operationType: 'avg',
+              sourceField: 'myfield',
+            },
+          },
+        },
+        b: {
+          indexPatternId: 'id-index-pattern-b',
+          columnOrder: ['col2'],
+          columns: {
+            col2: {
+              dataType: 'number',
+              isBucketed: false,
+              label: '',
+              operationType: 'avg',
+              sourceField: 'myfield2',
+            },
+          },
+        },
+      },
+      isFirstExistenceFetch: false,
+    };
+
+    it('should create a reference for each layer and for current index pattern', () => {
+      const { savedObjectReferences } = extractReferences(state);
+      expect(savedObjectReferences).toMatchInlineSnapshot(`
+        Array [
+          Object {
+            "id": "b",
+            "name": "indexpattern-datasource-current-indexpattern",
+            "type": "index-pattern",
+          },
+          Object {
+            "id": "id-index-pattern-a",
+            "name": "indexpattern-datasource-layer-a",
+            "type": "index-pattern",
+          },
+          Object {
+            "id": "id-index-pattern-b",
+            "name": "indexpattern-datasource-layer-b",
+            "type": "index-pattern",
+          },
+        ]
+      `);
+    });
+
+    it('should restore layers', () => {
+      const { savedObjectReferences, state: persistedState } = extractReferences(state);
+      expect(injectReferences(persistedState, savedObjectReferences).layers).toEqual(state.layers);
+    });
+
+    it('should restore current index pattern', () => {
+      const { savedObjectReferences, state: persistedState } = extractReferences(state);
+      expect(injectReferences(persistedState, savedObjectReferences).currentIndexPatternId).toEqual(
+        state.currentIndexPatternId
+      );
+    });
+  });
+
   describe('changeIndexPattern', () => {
     it('loads the index pattern and then sets it as current', async () => {
       const setState = jest.fn();
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/loader.ts b/x-pack/plugins/lens/public/indexpattern_datasource/loader.ts
index 9c4a19e58a052..24906790a9fc9 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/loader.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/loader.ts
@@ -6,7 +6,7 @@
 
 import _ from 'lodash';
 import { IStorageWrapper } from 'src/plugins/kibana_utils/public';
-import { SavedObjectsClientContract, HttpSetup } from 'kibana/public';
+import { SavedObjectsClientContract, HttpSetup, SavedObjectReference } from 'kibana/public';
 import { StateSetter } from '../types';
 import {
   IndexPattern,
@@ -14,6 +14,7 @@ import {
   IndexPatternPersistedState,
   IndexPatternPrivateState,
   IndexPatternField,
+  IndexPatternLayer,
 } from './types';
 import { updateLayerIndexPattern } from './state_helpers';
 import { DateRange, ExistingFields } from '../../common/types';
@@ -115,14 +116,58 @@ const setLastUsedIndexPatternId = (storage: IStorageWrapper, value: string) => {
   writeToStorage(storage, 'indexPatternId', value);
 };
 
+const CURRENT_PATTERN_REFERENCE_NAME = 'indexpattern-datasource-current-indexpattern';
+function getLayerReferenceName(layerId: string) {
+  return `indexpattern-datasource-layer-${layerId}`;
+}
+
+export function extractReferences({ currentIndexPatternId, layers }: IndexPatternPrivateState) {
+  const savedObjectReferences: SavedObjectReference[] = [];
+  savedObjectReferences.push({
+    type: 'index-pattern',
+    id: currentIndexPatternId,
+    name: CURRENT_PATTERN_REFERENCE_NAME,
+  });
+  const persistableLayers: Record<string, Omit<IndexPatternLayer, 'indexPatternId'>> = {};
+  Object.entries(layers).forEach(([layerId, { indexPatternId, ...persistableLayer }]) => {
+    savedObjectReferences.push({
+      type: 'index-pattern',
+      id: indexPatternId,
+      name: getLayerReferenceName(layerId),
+    });
+    persistableLayers[layerId] = persistableLayer;
+  });
+  return { savedObjectReferences, state: { layers: persistableLayers } };
+}
+
+export function injectReferences(
+  state: IndexPatternPersistedState,
+  references: SavedObjectReference[]
+) {
+  const layers: Record<string, IndexPatternLayer> = {};
+  Object.entries(state.layers).forEach(([layerId, persistedLayer]) => {
+    layers[layerId] = {
+      ...persistedLayer,
+      indexPatternId: references.find(({ name }) => name === getLayerReferenceName(layerId))!.id,
+    };
+  });
+  return {
+    currentIndexPatternId: references.find(({ name }) => name === CURRENT_PATTERN_REFERENCE_NAME)!
+      .id,
+    layers,
+  };
+}
+
 export async function loadInitialState({
-  state,
+  persistedState,
+  references,
   savedObjectsClient,
   defaultIndexPatternId,
   storage,
   indexPatternsService,
 }: {
-  state?: IndexPatternPersistedState;
+  persistedState?: IndexPatternPersistedState;
+  references?: SavedObjectReference[];
   savedObjectsClient: SavedObjectsClient;
   defaultIndexPatternId?: string;
   storage: IStorageWrapper;
@@ -131,6 +176,9 @@ export async function loadInitialState({
   const indexPatternRefs = await loadIndexPatternRefs(savedObjectsClient);
   const lastUsedIndexPatternId = getLastUsedIndexPatternId(storage, indexPatternRefs);
 
+  const state =
+    persistedState && references ? injectReferences(persistedState, references) : undefined;
+
   const requiredPatterns = _.uniq(
     state
       ? Object.values(state.layers)
diff --git a/x-pack/plugins/lens/public/indexpattern_datasource/types.ts b/x-pack/plugins/lens/public/indexpattern_datasource/types.ts
index 8d0e82b176aa9..95cc47e68f8a1 100644
--- a/x-pack/plugins/lens/public/indexpattern_datasource/types.ts
+++ b/x-pack/plugins/lens/public/indexpattern_datasource/types.ts
@@ -40,11 +40,12 @@ export interface IndexPatternLayer {
 }
 
 export interface IndexPatternPersistedState {
-  currentIndexPatternId: string;
-  layers: Record<string, IndexPatternLayer>;
+  layers: Record<string, Omit<IndexPatternLayer, 'indexPatternId'>>;
 }
 
-export type IndexPatternPrivateState = IndexPatternPersistedState & {
+export interface IndexPatternPrivateState {
+  currentIndexPatternId: string;
+  layers: Record<string, IndexPatternLayer>;
   indexPatternRefs: IndexPatternRef[];
   indexPatterns: Record<string, IndexPattern>;
 
@@ -54,7 +55,7 @@ export type IndexPatternPrivateState = IndexPatternPersistedState & {
   existingFields: Record<string, Record<string, boolean>>;
   isFirstExistenceFetch: boolean;
   existenceFetchFailed?: boolean;
-};
+}
 
 export interface IndexPatternRef {
   id: string;
diff --git a/x-pack/plugins/lens/public/metric_visualization/metric_visualization.test.ts b/x-pack/plugins/lens/public/metric_visualization/metric_visualization.test.ts
index 62f47a21c85b0..f3c9a725ee2e2 100644
--- a/x-pack/plugins/lens/public/metric_visualization/metric_visualization.test.ts
+++ b/x-pack/plugins/lens/public/metric_visualization/metric_visualization.test.ts
@@ -66,12 +66,6 @@ describe('metric_visualization', () => {
     });
   });
 
-  describe('#getPersistableState', () => {
-    it('persists the state as given', () => {
-      expect(metricVisualization.getPersistableState(exampleState())).toEqual(exampleState());
-    });
-  });
-
   describe('#getConfiguration', () => {
     it('can add a metric when there is no accessor', () => {
       expect(
@@ -168,7 +162,8 @@ describe('metric_visualization', () => {
         datasourceLayers: { l1: datasource },
       };
 
-      expect(metricVisualization.toExpression(exampleState(), frame)).toMatchInlineSnapshot(`
+      expect(metricVisualization.toExpression(exampleState(), frame.datasourceLayers))
+        .toMatchInlineSnapshot(`
         Object {
           "chain": Array [
             Object {
diff --git a/x-pack/plugins/lens/public/metric_visualization/metric_visualization.tsx b/x-pack/plugins/lens/public/metric_visualization/metric_visualization.tsx
index e565d2fa8b293..5f1ce5334dd36 100644
--- a/x-pack/plugins/lens/public/metric_visualization/metric_visualization.tsx
+++ b/x-pack/plugins/lens/public/metric_visualization/metric_visualization.tsx
@@ -7,20 +7,20 @@
 import { i18n } from '@kbn/i18n';
 import { Ast } from '@kbn/interpreter/target/common';
 import { getSuggestions } from './metric_suggestions';
-import { Visualization, FramePublicAPI, OperationMetadata } from '../types';
-import { State, PersistableState } from './types';
+import { Visualization, OperationMetadata, DatasourcePublicAPI } from '../types';
+import { State } from './types';
 import chartMetricSVG from '../assets/chart_metric.svg';
 
 const toExpression = (
   state: State,
-  frame: FramePublicAPI,
+  datasourceLayers: Record<string, DatasourcePublicAPI>,
   mode: 'reduced' | 'full' = 'full'
 ): Ast | null => {
   if (!state.accessor) {
     return null;
   }
 
-  const [datasource] = Object.values(frame.datasourceLayers);
+  const [datasource] = Object.values(datasourceLayers);
   const operation = datasource && datasource.getOperationForColumnId(state.accessor);
 
   return {
@@ -39,7 +39,7 @@ const toExpression = (
   };
 };
 
-export const metricVisualization: Visualization<State, PersistableState> = {
+export const metricVisualization: Visualization<State> = {
   id: 'lnsMetric',
 
   visualizationTypes: [
@@ -88,8 +88,6 @@ export const metricVisualization: Visualization<State, PersistableState> = {
     );
   },
 
-  getPersistableState: (state) => state,
-
   getConfiguration(props) {
     return {
       groups: [
@@ -106,8 +104,8 @@ export const metricVisualization: Visualization<State, PersistableState> = {
   },
 
   toExpression,
-  toPreviewExpression: (state: State, frame: FramePublicAPI) =>
-    toExpression(state, frame, 'reduced'),
+  toPreviewExpression: (state, datasourceLayers) =>
+    toExpression(state, datasourceLayers, 'reduced'),
 
   setDimension({ prevState, columnId }) {
     return { ...prevState, accessor: columnId };
diff --git a/x-pack/plugins/lens/public/metric_visualization/types.ts b/x-pack/plugins/lens/public/metric_visualization/types.ts
index 53fc103934255..86a781716b345 100644
--- a/x-pack/plugins/lens/public/metric_visualization/types.ts
+++ b/x-pack/plugins/lens/public/metric_visualization/types.ts
@@ -13,5 +13,3 @@ export interface MetricConfig extends State {
   title: string;
   mode: 'reduced' | 'full';
 }
-
-export type PersistableState = State;
diff --git a/x-pack/plugins/lens/public/persistence/filter_references.test.ts b/x-pack/plugins/lens/public/persistence/filter_references.test.ts
new file mode 100644
index 0000000000000..23c0cd1d11f1b
--- /dev/null
+++ b/x-pack/plugins/lens/public/persistence/filter_references.test.ts
@@ -0,0 +1,99 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License;
+ * you may not use this file except in compliance with the Elastic License.
+ */
+
+import { Filter } from 'src/plugins/data/public';
+import { extractFilterReferences, injectFilterReferences } from './filter_references';
+import { FilterStateStore } from 'src/plugins/data/common';
+
+describe('filter saved object references', () => {
+  const filters: Filter[] = [
+    {
+      $state: { store: FilterStateStore.APP_STATE },
+      meta: {
+        alias: null,
+        disabled: false,
+        index: '90943e30-9a47-11e8-b64d-95841ca0b247',
+        key: 'geo.src',
+        negate: true,
+        params: { query: 'CN' },
+        type: 'phrase',
+      },
+      query: { match_phrase: { 'geo.src': 'CN' } },
+    },
+    {
+      $state: { store: FilterStateStore.APP_STATE },
+      meta: {
+        alias: null,
+        disabled: false,
+        index: 'ff959d40-b880-11e8-a6d9-e546fe2bba5f',
+        key: 'geoip.country_iso_code',
+        negate: true,
+        params: { query: 'US' },
+        type: 'phrase',
+      },
+      query: { match_phrase: { 'geoip.country_iso_code': 'US' } },
+    },
+  ];
+
+  it('should create two index-pattern references', () => {
+    const { references } = extractFilterReferences(filters);
+    expect(references).toMatchInlineSnapshot(`
+      Array [
+        Object {
+          "id": "90943e30-9a47-11e8-b64d-95841ca0b247",
+          "name": "filter-index-pattern-0",
+          "type": "index-pattern",
+        },
+        Object {
+          "id": "ff959d40-b880-11e8-a6d9-e546fe2bba5f",
+          "name": "filter-index-pattern-1",
+          "type": "index-pattern",
+        },
+      ]
+    `);
+  });
+
+  it('should restore the same filter after extracting and injecting', () => {
+    const { persistableFilters, references } = extractFilterReferences(filters);
+    expect(injectFilterReferences(persistableFilters, references)).toEqual(filters);
+  });
+
+  it('should ignore other references', () => {
+    const { persistableFilters, references } = extractFilterReferences(filters);
+    expect(
+      injectFilterReferences(persistableFilters, [
+        { type: 'index-pattern', id: '1234', name: 'some other index pattern' },
+        ...references,
+      ])
+    ).toEqual(filters);
+  });
+
+  it('should inject other ids if references change', () => {
+    const { persistableFilters, references } = extractFilterReferences(filters);
+
+    expect(
+      injectFilterReferences(
+        persistableFilters,
+        references.map((reference, index) => ({ ...reference, id: `overwritten-id-${index}` }))
+      )
+    ).toEqual([
+      {
+        ...filters[0],
+        meta: {
+          ...filters[0].meta,
+          index: 'overwritten-id-0',
+        },
+      },
+      {
+        ...filters[1],
+        meta: {
+          ...filters[1].meta,
+          index: 'overwritten-id-1',
+        },
+      },
+    ]);
+  });
+});
diff --git a/x-pack/plugins/lens/public/persistence/filter_references.ts b/x-pack/plugins/lens/public/persistence/filter_references.ts
new file mode 100644
index 0000000000000..47564e510ce9c
--- /dev/null
+++ b/x-pack/plugins/lens/public/persistence/filter_references.ts
@@ -0,0 +1,56 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License;
+ * you may not use this file except in compliance with the Elastic License.
+ */
+
+import { Filter } from 'src/plugins/data/public';
+import { SavedObjectReference } from 'kibana/public';
+import { PersistableFilter } from '../../common';
+
+export function extractFilterReferences(
+  filters: Filter[]
+): { persistableFilters: PersistableFilter[]; references: SavedObjectReference[] } {
+  const references: SavedObjectReference[] = [];
+  const persistableFilters = filters.map((filterRow, i) => {
+    if (!filterRow.meta || !filterRow.meta.index) {
+      return filterRow;
+    }
+    const refName = `filter-index-pattern-${i}`;
+    references.push({
+      name: refName,
+      type: 'index-pattern',
+      id: filterRow.meta.index,
+    });
+    return {
+      ...filterRow,
+      meta: {
+        ...filterRow.meta,
+        indexRefName: refName,
+        index: undefined,
+      },
+    };
+  });
+
+  return { persistableFilters, references };
+}
+
+export function injectFilterReferences(
+  filters: PersistableFilter[],
+  references: SavedObjectReference[]
+) {
+  return filters.map((filterRow) => {
+    if (!filterRow.meta || !filterRow.meta.indexRefName) {
+      return filterRow as Filter;
+    }
+    const { indexRefName, ...metaRest } = filterRow.meta;
+    const reference = references.find((ref) => ref.name === indexRefName);
+    if (!reference) {
+      throw new Error(`Could not find reference for ${indexRefName}`);
+    }
+    return {
+      ...filterRow,
+      meta: { ...metaRest, index: reference.id },
+    };
+  });
+}
diff --git a/x-pack/plugins/lens/public/persistence/index.ts b/x-pack/plugins/lens/public/persistence/index.ts
index 1f823ff75c8c6..464bd46790422 100644
--- a/x-pack/plugins/lens/public/persistence/index.ts
+++ b/x-pack/plugins/lens/public/persistence/index.ts
@@ -5,3 +5,4 @@
  */
 
 export * from './saved_object_store';
+export * from './filter_references';
diff --git a/x-pack/plugins/lens/public/persistence/saved_object_store.test.ts b/x-pack/plugins/lens/public/persistence/saved_object_store.test.ts
index f8f8d889233a7..ba7c0ee6ae786 100644
--- a/x-pack/plugins/lens/public/persistence/saved_object_store.test.ts
+++ b/x-pack/plugins/lens/public/persistence/saved_object_store.test.ts
@@ -30,11 +30,8 @@ describe('LensStore', () => {
         title: 'Hello',
         description: 'My doc',
         visualizationType: 'bar',
-        expression: '',
+        references: [],
         state: {
-          datasourceMetaData: {
-            filterableIndexPatterns: [],
-          },
           datasourceStates: {
             indexpattern: { type: 'index_pattern', indexPattern: '.kibana_test' },
           },
@@ -49,11 +46,8 @@ describe('LensStore', () => {
         title: 'Hello',
         description: 'My doc',
         visualizationType: 'bar',
-        expression: '',
+        references: [],
         state: {
-          datasourceMetaData: {
-            filterableIndexPatterns: [],
-          },
           datasourceStates: {
             indexpattern: { type: 'index_pattern', indexPattern: '.kibana_test' },
           },
@@ -64,21 +58,25 @@ describe('LensStore', () => {
       });
 
       expect(client.create).toHaveBeenCalledTimes(1);
-      expect(client.create).toHaveBeenCalledWith('lens', {
-        title: 'Hello',
-        description: 'My doc',
-        visualizationType: 'bar',
-        expression: '',
-        state: {
-          datasourceMetaData: { filterableIndexPatterns: [] },
-          datasourceStates: {
-            indexpattern: { type: 'index_pattern', indexPattern: '.kibana_test' },
+      expect(client.create).toHaveBeenCalledWith(
+        'lens',
+        {
+          title: 'Hello',
+          description: 'My doc',
+          visualizationType: 'bar',
+          state: {
+            datasourceStates: {
+              indexpattern: { type: 'index_pattern', indexPattern: '.kibana_test' },
+            },
+            visualization: { x: 'foo', y: 'baz' },
+            query: { query: '', language: 'lucene' },
+            filters: [],
           },
-          visualization: { x: 'foo', y: 'baz' },
-          query: { query: '', language: 'lucene' },
-          filters: [],
         },
-      });
+        {
+          references: [],
+        }
+      );
     });
 
     test('updates and returns a visualization document', async () => {
@@ -87,9 +85,8 @@ describe('LensStore', () => {
         id: 'Gandalf',
         title: 'Even the very wise cannot see all ends.',
         visualizationType: 'line',
-        expression: '',
+        references: [],
         state: {
-          datasourceMetaData: { filterableIndexPatterns: [] },
           datasourceStates: { indexpattern: { type: 'index_pattern', indexPattern: 'lotr' } },
           visualization: { gear: ['staff', 'pointy hat'] },
           query: { query: '', language: 'lucene' },
@@ -101,9 +98,8 @@ describe('LensStore', () => {
         id: 'Gandalf',
         title: 'Even the very wise cannot see all ends.',
         visualizationType: 'line',
-        expression: '',
+        references: [],
         state: {
-          datasourceMetaData: { filterableIndexPatterns: [] },
           datasourceStates: { indexpattern: { type: 'index_pattern', indexPattern: 'lotr' } },
           visualization: { gear: ['staff', 'pointy hat'] },
           query: { query: '', language: 'lucene' },
@@ -116,22 +112,21 @@ describe('LensStore', () => {
         {
           type: 'lens',
           id: 'Gandalf',
+          references: [],
           attributes: {
             title: null,
             visualizationType: null,
-            expression: null,
             state: null,
           },
         },
         {
           type: 'lens',
           id: 'Gandalf',
+          references: [],
           attributes: {
             title: 'Even the very wise cannot see all ends.',
             visualizationType: 'line',
-            expression: '',
             state: {
-              datasourceMetaData: { filterableIndexPatterns: [] },
               datasourceStates: { indexpattern: { type: 'index_pattern', indexPattern: 'lotr' } },
               visualization: { gear: ['staff', 'pointy hat'] },
               query: { query: '', language: 'lucene' },
diff --git a/x-pack/plugins/lens/public/persistence/saved_object_store.ts b/x-pack/plugins/lens/public/persistence/saved_object_store.ts
index 59ead53956a8d..e4609213ec792 100644
--- a/x-pack/plugins/lens/public/persistence/saved_object_store.ts
+++ b/x-pack/plugins/lens/public/persistence/saved_object_store.ts
@@ -4,8 +4,13 @@
  * you may not use this file except in compliance with the Elastic License.
  */
 
-import { SavedObjectAttributes, SavedObjectsClientContract } from 'kibana/public';
-import { Query, Filter } from '../../../../../src/plugins/data/public';
+import {
+  SavedObjectAttributes,
+  SavedObjectsClientContract,
+  SavedObjectReference,
+} from 'kibana/public';
+import { Query } from '../../../../../src/plugins/data/public';
+import { PersistableFilter } from '../../common';
 
 export interface Document {
   id?: string;
@@ -13,16 +18,13 @@ export interface Document {
   visualizationType: string | null;
   title: string;
   description?: string;
-  expression: string | null;
   state: {
-    datasourceMetaData: {
-      filterableIndexPatterns: Array<{ id: string; title: string }>;
-    };
     datasourceStates: Record<string, unknown>;
     visualization: unknown;
     query: Query;
-    filters: Filter[];
+    filters: PersistableFilter[];
   };
+  references: SavedObjectReference[];
 }
 
 export const DOC_TYPE = 'lens';
@@ -45,14 +47,16 @@ export class SavedObjectIndexStore implements SavedObjectStore {
   }
 
   async save(vis: Document) {
-    const { id, type, ...rest } = vis;
+    const { id, type, references, ...rest } = vis;
     // TODO: SavedObjectAttributes should support this kind of object,
     // remove this workaround when SavedObjectAttributes is updated.
     const attributes = (rest as unknown) as SavedObjectAttributes;
 
     const result = await (id
-      ? this.safeUpdate(id, attributes)
-      : this.client.create(DOC_TYPE, attributes));
+      ? this.safeUpdate(id, attributes, references)
+      : this.client.create(DOC_TYPE, attributes, {
+          references,
+        }));
 
     return { ...vis, id: result.id };
   }
@@ -63,21 +67,25 @@ export class SavedObjectIndexStore implements SavedObjectStore {
   // deleted subtrees make it back into the object after a load.
   // This function fixes this by doing two updates - one to empty out the document setting
   // every key to null, and a second one to load the new content.
-  private async safeUpdate(id: string, attributes: SavedObjectAttributes) {
+  private async safeUpdate(
+    id: string,
+    attributes: SavedObjectAttributes,
+    references: SavedObjectReference[]
+  ) {
     const resetAttributes: SavedObjectAttributes = {};
     Object.keys(attributes).forEach((key) => {
       resetAttributes[key] = null;
     });
     return (
       await this.client.bulkUpdate([
-        { type: DOC_TYPE, id, attributes: resetAttributes },
-        { type: DOC_TYPE, id, attributes },
+        { type: DOC_TYPE, id, attributes: resetAttributes, references },
+        { type: DOC_TYPE, id, attributes, references },
       ])
     ).savedObjects[1];
   }
 
   async load(id: string): Promise<Document> {
-    const { type, attributes, error } = await this.client.get(DOC_TYPE, id);
+    const { type, attributes, references, error } = await this.client.get(DOC_TYPE, id);
 
     if (error) {
       throw error;
@@ -85,6 +93,7 @@ export class SavedObjectIndexStore implements SavedObjectStore {
 
     return {
       ...(attributes as SavedObjectAttributes),
+      references,
       id,
       type,
     } as Document;
diff --git a/x-pack/plugins/lens/public/pie_visualization/pie_visualization.tsx b/x-pack/plugins/lens/public/pie_visualization/pie_visualization.tsx
index 5a68516db6aa3..855bacd4f794c 100644
--- a/x-pack/plugins/lens/public/pie_visualization/pie_visualization.tsx
+++ b/x-pack/plugins/lens/public/pie_visualization/pie_visualization.tsx
@@ -31,7 +31,7 @@ const bucketedOperations = (op: OperationMetadata) => op.isBucketed;
 const numberMetricOperations = (op: OperationMetadata) =>
   !op.isBucketed && op.dataType === 'number';
 
-export const pieVisualization: Visualization<PieVisualizationState, PieVisualizationState> = {
+export const pieVisualization: Visualization<PieVisualizationState> = {
   id: 'lnsPie',
 
   visualizationTypes: [
@@ -91,8 +91,6 @@ export const pieVisualization: Visualization<PieVisualizationState, PieVisualiza
     );
   },
 
-  getPersistableState: (state) => state,
-
   getSuggestions: suggestions,
 
   getConfiguration({ state, frame, layerId }) {
diff --git a/x-pack/plugins/lens/public/pie_visualization/to_expression.ts b/x-pack/plugins/lens/public/pie_visualization/to_expression.ts
index fbc47e8bfb00f..f36b9efb930a9 100644
--- a/x-pack/plugins/lens/public/pie_visualization/to_expression.ts
+++ b/x-pack/plugins/lens/public/pie_visualization/to_expression.ts
@@ -5,21 +5,24 @@
  */
 
 import { Ast } from '@kbn/interpreter/common';
-import { FramePublicAPI, Operation } from '../types';
+import { Operation, DatasourcePublicAPI } from '../types';
 import { DEFAULT_PERCENT_DECIMALS } from './constants';
 import { PieVisualizationState } from './types';
 
-export function toExpression(state: PieVisualizationState, frame: FramePublicAPI) {
-  return expressionHelper(state, frame, false);
+export function toExpression(
+  state: PieVisualizationState,
+  datasourceLayers: Record<string, DatasourcePublicAPI>
+) {
+  return expressionHelper(state, datasourceLayers, false);
 }
 
 function expressionHelper(
   state: PieVisualizationState,
-  frame: FramePublicAPI,
+  datasourceLayers: Record<string, DatasourcePublicAPI>,
   isPreview: boolean
 ): Ast | null {
   const layer = state.layers[0];
-  const datasource = frame.datasourceLayers[layer.layerId];
+  const datasource = datasourceLayers[layer.layerId];
   const operations = layer.groups
     .map((columnId) => ({ columnId, operation: datasource.getOperationForColumnId(columnId) }))
     .filter((o): o is { columnId: string; operation: Operation } => !!o.operation);
@@ -50,6 +53,9 @@ function expressionHelper(
   };
 }
 
-export function toPreviewExpression(state: PieVisualizationState, frame: FramePublicAPI) {
-  return expressionHelper(state, frame, true);
+export function toPreviewExpression(
+  state: PieVisualizationState,
+  datasourceLayers: Record<string, DatasourcePublicAPI>
+) {
+  return expressionHelper(state, datasourceLayers, true);
 }
diff --git a/x-pack/plugins/lens/public/types.ts b/x-pack/plugins/lens/public/types.ts
index c7bda65cd1327..20f2ce6c56774 100644
--- a/x-pack/plugins/lens/public/types.ts
+++ b/x-pack/plugins/lens/public/types.ts
@@ -7,6 +7,7 @@
 import { Ast } from '@kbn/interpreter/common';
 import { IconType } from '@elastic/eui/src/components/icon/icon';
 import { CoreSetup } from 'kibana/public';
+import { SavedObjectReference } from 'kibana/public';
 import {
   ExpressionRendererEvent,
   IInterpreterRenderHandlers,
@@ -30,7 +31,6 @@ export type FormatFactory = (mapping?: SerializedFieldFormat) => IFieldFormat;
 export interface PublicAPIProps<T> {
   state: T;
   layerId: string;
-  dateRange: DateRange;
 }
 
 export interface EditorFrameProps {
@@ -44,8 +44,9 @@ export interface EditorFrameProps {
   // Frame loader (app or embeddable) is expected to call this when it loads and updates
   // This should be replaced with a top-down state
   onChange: (newState: {
-    filterableIndexPatterns: DatasourceMetaData['filterableIndexPatterns'];
+    filterableIndexPatterns: string[];
     doc: Document;
+    isSaveable: boolean;
   }) => void;
   showNoDataPopover: () => void;
 }
@@ -57,9 +58,7 @@ export interface EditorFrameInstance {
 export interface EditorFrameSetup {
   // generic type on the API functions to pull the "unknown vs. specific type" error into the implementation
   registerDatasource: <T, P>(datasource: Datasource<T, P> | Promise<Datasource<T, P>>) => void;
-  registerVisualization: <T, P>(
-    visualization: Visualization<T, P> | Promise<Visualization<T, P>>
-  ) => void;
+  registerVisualization: <T>(visualization: Visualization<T> | Promise<Visualization<T>>) => void;
 }
 
 export interface EditorFrameStart {
@@ -131,10 +130,6 @@ export interface DatasourceSuggestion<T = unknown> {
   keptLayerIds: string[];
 }
 
-export interface DatasourceMetaData {
-  filterableIndexPatterns: Array<{ id: string; title: string }>;
-}
-
 export type StateSetter<T> = (newState: T | ((prevState: T) => T)) => void;
 
 /**
@@ -146,10 +141,10 @@ export interface Datasource<T = unknown, P = unknown> {
   // For initializing, either from an empty state or from persisted state
   // Because this will be called at runtime, state might have a type of `any` and
   // datasources should validate their arguments
-  initialize: (state?: P) => Promise<T>;
+  initialize: (state?: P, savedObjectReferences?: SavedObjectReference[]) => Promise<T>;
 
   // Given the current state, which parts should be saved?
-  getPersistableState: (state: T) => P;
+  getPersistableState: (state: T) => { state: P; savedObjectReferences: SavedObjectReference[] };
 
   insertLayer: (state: T, newLayerId: string) => T;
   removeLayer: (state: T, layerId: string) => T;
@@ -166,8 +161,6 @@ export interface Datasource<T = unknown, P = unknown> {
 
   toExpression: (state: T, layerId: string) => Ast | string | null;
 
-  getMetaData: (state: T) => DatasourceMetaData;
-
   getDatasourceSuggestionsForField: (state: T, field: unknown) => Array<DatasourceSuggestion<T>>;
   getDatasourceSuggestionsFromCurrentState: (state: T) => Array<DatasourceSuggestion<T>>;
 
@@ -408,7 +401,7 @@ export interface VisualizationType {
   label: string;
 }
 
-export interface Visualization<T = unknown, P = unknown> {
+export interface Visualization<T = unknown> {
   /** Plugin ID, such as "lnsXY" */
   id: string;
 
@@ -418,11 +411,7 @@ export interface Visualization<T = unknown, P = unknown> {
    * - Loadingn from a saved visualization
    * - When using suggestions, the suggested state is passed in
    */
-  initialize: (frame: FramePublicAPI, state?: P) => T;
-  /**
-   * Can remove any state that should not be persisted to saved object, such as UI state
-   */
-  getPersistableState: (state: T) => P;
+  initialize: (frame: FramePublicAPI, state?: T) => T;
 
   /**
    * Visualizations must provide at least one type for the chart switcher,
@@ -504,12 +493,18 @@ export interface Visualization<T = unknown, P = unknown> {
    */
   getSuggestions: (context: SuggestionRequest<T>) => Array<VisualizationSuggestion<T>>;
 
-  toExpression: (state: T, frame: FramePublicAPI) => Ast | string | null;
+  toExpression: (
+    state: T,
+    datasourceLayers: Record<string, DatasourcePublicAPI>
+  ) => Ast | string | null;
   /**
    * Expression to render a preview version of the chart in very constrained space.
    * If there is no expression provided, the preview icon is used.
    */
-  toPreviewExpression?: (state: T, frame: FramePublicAPI) => Ast | string | null;
+  toPreviewExpression?: (
+    state: T,
+    datasourceLayers: Record<string, DatasourcePublicAPI>
+  ) => Ast | string | null;
 }
 
 export interface LensFilterEvent {
diff --git a/x-pack/plugins/lens/public/xy_visualization/to_expression.test.ts b/x-pack/plugins/lens/public/xy_visualization/to_expression.test.ts
index 876d1141740e1..f579085646f6f 100644
--- a/x-pack/plugins/lens/public/xy_visualization/to_expression.test.ts
+++ b/x-pack/plugins/lens/public/xy_visualization/to_expression.test.ts
@@ -53,7 +53,7 @@ describe('#toExpression', () => {
             },
           ],
         },
-        frame
+        frame.datasourceLayers
       )
     ).toMatchSnapshot();
   });
@@ -74,7 +74,7 @@ describe('#toExpression', () => {
             },
           ],
         },
-        frame
+        frame.datasourceLayers
       ) as Ast).chain[0].arguments.fittingFunction[0]
     ).toEqual('None');
   });
@@ -94,7 +94,7 @@ describe('#toExpression', () => {
           },
         ],
       },
-      frame
+      frame.datasourceLayers
     ) as Ast;
     expect(expression.chain[0].arguments.showXAxisTitle[0]).toBe(true);
     expect(expression.chain[0].arguments.showYAxisTitle[0]).toBe(true);
@@ -116,7 +116,7 @@ describe('#toExpression', () => {
             },
           ],
         },
-        frame
+        frame.datasourceLayers
       )
     ).toBeNull();
   });
@@ -137,7 +137,7 @@ describe('#toExpression', () => {
             },
           ],
         },
-        frame
+        frame.datasourceLayers
       )
     ).toBeNull();
   });
@@ -157,7 +157,7 @@ describe('#toExpression', () => {
           },
         ],
       },
-      frame
+      frame.datasourceLayers
     )! as Ast;
 
     expect(mockDatasource.publicAPIMock.getOperationForColumnId).toHaveBeenCalledWith('b');
@@ -191,7 +191,7 @@ describe('#toExpression', () => {
           },
         ],
       },
-      frame
+      frame.datasourceLayers
     ) as Ast;
     expect(
       (expression.chain[0].arguments.tickLabelsVisibilitySettings[0] as Ast).chain[0].arguments
@@ -216,7 +216,7 @@ describe('#toExpression', () => {
           },
         ],
       },
-      frame
+      frame.datasourceLayers
     ) as Ast;
     expect(
       (expression.chain[0].arguments.gridlinesVisibilitySettings[0] as Ast).chain[0].arguments
diff --git a/x-pack/plugins/lens/public/xy_visualization/to_expression.ts b/x-pack/plugins/lens/public/xy_visualization/to_expression.ts
index 9b9c159af265e..cd32d4f94c3e5 100644
--- a/x-pack/plugins/lens/public/xy_visualization/to_expression.ts
+++ b/x-pack/plugins/lens/public/xy_visualization/to_expression.ts
@@ -7,13 +7,16 @@
 import { Ast } from '@kbn/interpreter/common';
 import { ScaleType } from '@elastic/charts';
 import { State, LayerConfig } from './types';
-import { FramePublicAPI, OperationMetadata } from '../types';
+import { OperationMetadata, DatasourcePublicAPI } from '../types';
 
 interface ValidLayer extends LayerConfig {
   xAccessor: NonNullable<LayerConfig['xAccessor']>;
 }
 
-export const toExpression = (state: State, frame: FramePublicAPI): Ast | null => {
+export const toExpression = (
+  state: State,
+  datasourceLayers: Record<string, DatasourcePublicAPI>
+): Ast | null => {
   if (!state || !state.layers.length) {
     return null;
   }
@@ -21,19 +24,20 @@ export const toExpression = (state: State, frame: FramePublicAPI): Ast | null =>
   const metadata: Record<string, Record<string, OperationMetadata | null>> = {};
   state.layers.forEach((layer) => {
     metadata[layer.layerId] = {};
-    const datasource = frame.datasourceLayers[layer.layerId];
+    const datasource = datasourceLayers[layer.layerId];
     datasource.getTableSpec().forEach((column) => {
-      const operation = frame.datasourceLayers[layer.layerId].getOperationForColumnId(
-        column.columnId
-      );
+      const operation = datasourceLayers[layer.layerId].getOperationForColumnId(column.columnId);
       metadata[layer.layerId][column.columnId] = operation;
     });
   });
 
-  return buildExpression(state, metadata, frame);
+  return buildExpression(state, metadata, datasourceLayers);
 };
 
-export function toPreviewExpression(state: State, frame: FramePublicAPI) {
+export function toPreviewExpression(
+  state: State,
+  datasourceLayers: Record<string, DatasourcePublicAPI>
+) {
   return toExpression(
     {
       ...state,
@@ -44,7 +48,7 @@ export function toPreviewExpression(state: State, frame: FramePublicAPI) {
         isVisible: false,
       },
     },
-    frame
+    datasourceLayers
   );
 }
 
@@ -77,7 +81,7 @@ export function getScaleType(metadata: OperationMetadata | null, defaultScale: S
 export const buildExpression = (
   state: State,
   metadata: Record<string, Record<string, OperationMetadata | null>>,
-  frame?: FramePublicAPI
+  datasourceLayers?: Record<string, DatasourcePublicAPI>
 ): Ast | null => {
   const validLayers = state.layers.filter((layer): layer is ValidLayer =>
     Boolean(layer.xAccessor && layer.accessors.length)
@@ -149,8 +153,8 @@ export const buildExpression = (
           layers: validLayers.map((layer) => {
             const columnToLabel: Record<string, string> = {};
 
-            if (frame) {
-              const datasource = frame.datasourceLayers[layer.layerId];
+            if (datasourceLayers) {
+              const datasource = datasourceLayers[layer.layerId];
               layer.accessors
                 .concat(layer.splitAccessor ? [layer.splitAccessor] : [])
                 .forEach((accessor) => {
@@ -162,8 +166,8 @@ export const buildExpression = (
             }
 
             const xAxisOperation =
-              frame &&
-              frame.datasourceLayers[layer.layerId].getOperationForColumnId(layer.xAccessor);
+              datasourceLayers &&
+              datasourceLayers[layer.layerId].getOperationForColumnId(layer.xAccessor);
 
             const isHistogramDimension = Boolean(
               xAxisOperation &&
diff --git a/x-pack/plugins/lens/public/xy_visualization/types.ts b/x-pack/plugins/lens/public/xy_visualization/types.ts
index ab689ceb183be..2739ffe42f13f 100644
--- a/x-pack/plugins/lens/public/xy_visualization/types.ts
+++ b/x-pack/plugins/lens/public/xy_visualization/types.ts
@@ -339,7 +339,6 @@ export interface XYState {
 }
 
 export type State = XYState;
-export type PersistableState = XYState;
 
 export const visualizationTypes: VisualizationType[] = [
   {
diff --git a/x-pack/plugins/lens/public/xy_visualization/xy_visualization.test.ts b/x-pack/plugins/lens/public/xy_visualization/xy_visualization.test.ts
index 0a8e8bbe0c46f..53f7a23dcae98 100644
--- a/x-pack/plugins/lens/public/xy_visualization/xy_visualization.test.ts
+++ b/x-pack/plugins/lens/public/xy_visualization/xy_visualization.test.ts
@@ -157,12 +157,6 @@ describe('xy_visualization', () => {
     });
   });
 
-  describe('#getPersistableState', () => {
-    it('persists the state as given', () => {
-      expect(xyVisualization.getPersistableState(exampleState())).toEqual(exampleState());
-    });
-  });
-
   describe('#removeLayer', () => {
     it('removes the specified layer', () => {
       const prevState: State = {
diff --git a/x-pack/plugins/lens/public/xy_visualization/xy_visualization.tsx b/x-pack/plugins/lens/public/xy_visualization/xy_visualization.tsx
index f321e0962caa8..8c551c575764e 100644
--- a/x-pack/plugins/lens/public/xy_visualization/xy_visualization.tsx
+++ b/x-pack/plugins/lens/public/xy_visualization/xy_visualization.tsx
@@ -13,7 +13,7 @@ import { i18n } from '@kbn/i18n';
 import { getSuggestions } from './xy_suggestions';
 import { LayerContextMenu, XyToolbar, DimensionEditor } from './xy_config_panel';
 import { Visualization, OperationMetadata, VisualizationType } from '../types';
-import { State, PersistableState, SeriesType, visualizationTypes, LayerConfig } from './types';
+import { State, SeriesType, visualizationTypes, LayerConfig } from './types';
 import chartBarStackedSVG from '../assets/chart_bar_stacked.svg';
 import chartMixedSVG from '../assets/chart_mixed_xy.svg';
 import { isHorizontalChart } from './state_helpers';
@@ -74,7 +74,7 @@ function getDescription(state?: State) {
   };
 }
 
-export const xyVisualization: Visualization<State, PersistableState> = {
+export const xyVisualization: Visualization<State> = {
   id: 'lnsXY',
 
   visualizationTypes,
@@ -159,8 +159,6 @@ export const xyVisualization: Visualization<State, PersistableState> = {
     );
   },
 
-  getPersistableState: (state) => state,
-
   getConfiguration(props) {
     const layer = props.state.layers.find((l) => l.layerId === props.layerId)!;
     return {
diff --git a/x-pack/plugins/lens/server/__snapshots__/migrations.test.ts.snap b/x-pack/plugins/lens/server/__snapshots__/migrations.test.ts.snap
new file mode 100644
index 0000000000000..4979438dbd3d0
--- /dev/null
+++ b/x-pack/plugins/lens/server/__snapshots__/migrations.test.ts.snap
@@ -0,0 +1,188 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`Lens migrations 7.10.0 references should produce a valid document 1`] = `
+Object {
+  "attributes": Object {
+    "state": Object {
+      "datasourceStates": Object {
+        "indexpattern": Object {
+          "layers": Object {
+            "3b7791e9-326e-40d5-a787-b7594e48d906": Object {
+              "columnOrder": Array [
+                "77d8383e-f66e-471e-ae50-c427feedb5ba",
+                "a5c1b82d-51de-4448-a99d-6391432c3a03",
+              ],
+              "columns": Object {
+                "77d8383e-f66e-471e-ae50-c427feedb5ba": Object {
+                  "dataType": "string",
+                  "isBucketed": true,
+                  "label": "Top values of geoip.country_iso_code",
+                  "operationType": "terms",
+                  "params": Object {
+                    "orderBy": Object {
+                      "columnId": "a5c1b82d-51de-4448-a99d-6391432c3a03",
+                      "type": "column",
+                    },
+                    "orderDirection": "desc",
+                    "size": 5,
+                  },
+                  "scale": "ordinal",
+                  "sourceField": "geoip.country_iso_code",
+                },
+                "a5c1b82d-51de-4448-a99d-6391432c3a03": Object {
+                  "dataType": "number",
+                  "isBucketed": false,
+                  "label": "Count of records",
+                  "operationType": "count",
+                  "scale": "ratio",
+                  "sourceField": "Records",
+                },
+              },
+            },
+            "9a27f85d-35a9-4246-81b2-48e7ee9b0707": Object {
+              "columnOrder": Array [
+                "96352896-c508-4fca-90d8-66e9ebfce621",
+                "4ce9b4c7-2ebf-4d48-8669-0ea69d973353",
+              ],
+              "columns": Object {
+                "4ce9b4c7-2ebf-4d48-8669-0ea69d973353": Object {
+                  "dataType": "number",
+                  "isBucketed": false,
+                  "label": "Count of records",
+                  "operationType": "count",
+                  "scale": "ratio",
+                  "sourceField": "Records",
+                },
+                "96352896-c508-4fca-90d8-66e9ebfce621": Object {
+                  "dataType": "string",
+                  "isBucketed": true,
+                  "label": "Top values of geo.src",
+                  "operationType": "terms",
+                  "params": Object {
+                    "orderBy": Object {
+                      "columnId": "4ce9b4c7-2ebf-4d48-8669-0ea69d973353",
+                      "type": "column",
+                    },
+                    "orderDirection": "desc",
+                    "size": 5,
+                  },
+                  "scale": "ordinal",
+                  "sourceField": "geo.src",
+                },
+              },
+            },
+          },
+        },
+      },
+      "filters": Array [
+        Object {
+          "$state": Object {
+            "store": "appState",
+          },
+          "meta": Object {
+            "alias": null,
+            "disabled": false,
+            "index": undefined,
+            "indexRefName": "filter-index-pattern-0",
+            "key": "geo.src",
+            "negate": true,
+            "params": Object {
+              "query": "CN",
+            },
+            "type": "phrase",
+          },
+          "query": Object {
+            "match_phrase": Object {
+              "geo.src": "CN",
+            },
+          },
+        },
+        Object {
+          "$state": Object {
+            "store": "appState",
+          },
+          "meta": Object {
+            "alias": null,
+            "disabled": false,
+            "index": undefined,
+            "indexRefName": "filter-index-pattern-1",
+            "key": "geoip.country_iso_code",
+            "negate": true,
+            "params": Object {
+              "query": "US",
+            },
+            "type": "phrase",
+          },
+          "query": Object {
+            "match_phrase": Object {
+              "geoip.country_iso_code": "US",
+            },
+          },
+        },
+      ],
+      "query": Object {
+        "language": "kuery",
+        "query": "NOT bytes > 5000",
+      },
+      "visualization": Object {
+        "fittingFunction": "None",
+        "layers": Array [
+          Object {
+            "accessors": Array [
+              "4ce9b4c7-2ebf-4d48-8669-0ea69d973353",
+            ],
+            "layerId": "9a27f85d-35a9-4246-81b2-48e7ee9b0707",
+            "position": "top",
+            "seriesType": "bar",
+            "showGridlines": false,
+            "xAccessor": "96352896-c508-4fca-90d8-66e9ebfce621",
+          },
+          Object {
+            "accessors": Array [
+              "a5c1b82d-51de-4448-a99d-6391432c3a03",
+            ],
+            "layerId": "3b7791e9-326e-40d5-a787-b7594e48d906",
+            "seriesType": "bar",
+            "xAccessor": "77d8383e-f66e-471e-ae50-c427feedb5ba",
+          },
+        ],
+        "legend": Object {
+          "isVisible": true,
+          "position": "right",
+        },
+        "preferredSeriesType": "bar",
+      },
+    },
+    "title": "mylens",
+    "visualizationType": "lnsXY",
+  },
+  "references": Array [
+    Object {
+      "id": "ff959d40-b880-11e8-a6d9-e546fe2bba5f",
+      "name": "indexpattern-datasource-current-indexpattern",
+      "type": "index-pattern",
+    },
+    Object {
+      "id": "ff959d40-b880-11e8-a6d9-e546fe2bba5f",
+      "name": "indexpattern-datasource-layer-3b7791e9-326e-40d5-a787-b7594e48d906",
+      "type": "index-pattern",
+    },
+    Object {
+      "id": "90943e30-9a47-11e8-b64d-95841ca0b247",
+      "name": "indexpattern-datasource-layer-9a27f85d-35a9-4246-81b2-48e7ee9b0707",
+      "type": "index-pattern",
+    },
+    Object {
+      "id": "90943e30-9a47-11e8-b64d-95841ca0b247",
+      "name": "filter-index-pattern-0",
+      "type": "index-pattern",
+    },
+    Object {
+      "id": "ff959d40-b880-11e8-a6d9-e546fe2bba5f",
+      "name": "filter-index-pattern-1",
+      "type": "index-pattern",
+    },
+  ],
+  "type": "lens",
+}
+`;
diff --git a/x-pack/plugins/lens/server/migrations.test.ts b/x-pack/plugins/lens/server/migrations.test.ts
index 0541d9636577b..676494dcab619 100644
--- a/x-pack/plugins/lens/server/migrations.test.ts
+++ b/x-pack/plugins/lens/server/migrations.test.ts
@@ -278,4 +278,233 @@ describe('Lens migrations', () => {
       expect(result).toEqual(input);
     });
   });
+
+  describe('7.10.0 references', () => {
+    const context = {} as SavedObjectMigrationContext;
+
+    const example = {
+      attributes: {
+        description: '',
+        expression:
+          'kibana\n| kibana_context  query="{\\"query\\":\\"NOT bytes > 5000\\",\\"language\\":\\"kuery\\"}" \n  filters="[{\\"meta\\":{\\"index\\":\\"90943e30-9a47-11e8-b64d-95841ca0b247\\",\\"alias\\":null,\\"negate\\":true,\\"disabled\\":false,\\"type\\":\\"phrase\\",\\"key\\":\\"geo.src\\",\\"params\\":{\\"query\\":\\"CN\\"}},\\"query\\":{\\"match_phrase\\":{\\"geo.src\\":\\"CN\\"}},\\"$state\\":{\\"store\\":\\"appState\\"}},{\\"meta\\":{\\"index\\":\\"ff959d40-b880-11e8-a6d9-e546fe2bba5f\\",\\"alias\\":null,\\"negate\\":true,\\"disabled\\":false,\\"type\\":\\"phrase\\",\\"key\\":\\"geoip.country_iso_code\\",\\"params\\":{\\"query\\":\\"US\\"}},\\"query\\":{\\"match_phrase\\":{\\"geoip.country_iso_code\\":\\"US\\"}},\\"$state\\":{\\"store\\":\\"appState\\"}}]"\n| lens_merge_tables layerIds="9a27f85d-35a9-4246-81b2-48e7ee9b0707"\n  layerIds="3b7791e9-326e-40d5-a787-b7594e48d906" \n  tables={esaggs index="90943e30-9a47-11e8-b64d-95841ca0b247" metricsAtAllLevels=true partialRows=true includeFormatHints=true  aggConfigs="[{\\"id\\":\\"96352896-c508-4fca-90d8-66e9ebfce621\\",\\"enabled\\":true,\\"type\\":\\"terms\\",\\"schema\\":\\"segment\\",\\"params\\":{\\"field\\":\\"geo.src\\",\\"orderBy\\":\\"4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\",\\"order\\":\\"desc\\",\\"size\\":5,\\"otherBucket\\":false,\\"otherBucketLabel\\":\\"Other\\",\\"missingBucket\\":false,\\"missingBucketLabel\\":\\"Missing\\"}},{\\"id\\":\\"4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\",\\"enabled\\":true,\\"type\\":\\"count\\",\\"schema\\":\\"metric\\",\\"params\\":{}}]" | lens_rename_columns idMap="{\\"col-0-96352896-c508-4fca-90d8-66e9ebfce621\\":{\\"label\\":\\"Top values of geo.src\\",\\"dataType\\":\\"string\\",\\"operationType\\":\\"terms\\",\\"scale\\":\\"ordinal\\",\\"sourceField\\":\\"geo.src\\",\\"isBucketed\\":true,\\"params\\":{\\"size\\":5,\\"orderBy\\":{\\"type\\":\\"column\\",\\"columnId\\":\\"4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\"},\\"orderDirection\\":\\"desc\\"},\\"id\\":\\"96352896-c508-4fca-90d8-66e9ebfce621\\"},\\"col-1-4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\":{\\"label\\":\\"Count of records\\",\\"dataType\\":\\"number\\",\\"operationType\\":\\"count\\",\\"isBucketed\\":false,\\"scale\\":\\"ratio\\",\\"sourceField\\":\\"Records\\",\\"id\\":\\"4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\"}}"}\n  tables={esaggs index="ff959d40-b880-11e8-a6d9-e546fe2bba5f" metricsAtAllLevels=true partialRows=true includeFormatHints=true  aggConfigs="[{\\"id\\":\\"77d8383e-f66e-471e-ae50-c427feedb5ba\\",\\"enabled\\":true,\\"type\\":\\"terms\\",\\"schema\\":\\"segment\\",\\"params\\":{\\"field\\":\\"geoip.country_iso_code\\",\\"orderBy\\":\\"a5c1b82d-51de-4448-a99d-6391432c3a03\\",\\"order\\":\\"desc\\",\\"size\\":5,\\"otherBucket\\":false,\\"otherBucketLabel\\":\\"Other\\",\\"missingBucket\\":false,\\"missingBucketLabel\\":\\"Missing\\"}},{\\"id\\":\\"a5c1b82d-51de-4448-a99d-6391432c3a03\\",\\"enabled\\":true,\\"type\\":\\"count\\",\\"schema\\":\\"metric\\",\\"params\\":{}}]" | lens_rename_columns idMap="{\\"col-0-77d8383e-f66e-471e-ae50-c427feedb5ba\\":{\\"label\\":\\"Top values of geoip.country_iso_code\\",\\"dataType\\":\\"string\\",\\"operationType\\":\\"terms\\",\\"scale\\":\\"ordinal\\",\\"sourceField\\":\\"geoip.country_iso_code\\",\\"isBucketed\\":true,\\"params\\":{\\"size\\":5,\\"orderBy\\":{\\"type\\":\\"column\\",\\"columnId\\":\\"a5c1b82d-51de-4448-a99d-6391432c3a03\\"},\\"orderDirection\\":\\"desc\\"},\\"id\\":\\"77d8383e-f66e-471e-ae50-c427feedb5ba\\"},\\"col-1-a5c1b82d-51de-4448-a99d-6391432c3a03\\":{\\"label\\":\\"Count of records\\",\\"dataType\\":\\"number\\",\\"operationType\\":\\"count\\",\\"isBucketed\\":false,\\"scale\\":\\"ratio\\",\\"sourceField\\":\\"Records\\",\\"id\\":\\"a5c1b82d-51de-4448-a99d-6391432c3a03\\"}}"}\n| lens_xy_chart xTitle="Top values of geo.src" yTitle="Count of records" legend={lens_xy_legendConfig isVisible=true position="right"} fittingFunction="None" \n  layers={lens_xy_layer layerId="9a27f85d-35a9-4246-81b2-48e7ee9b0707" hide=false xAccessor="96352896-c508-4fca-90d8-66e9ebfce621" yScaleType="linear" xScaleType="ordinal" isHistogram=false   seriesType="bar" accessors="4ce9b4c7-2ebf-4d48-8669-0ea69d973353" columnToLabel="{\\"4ce9b4c7-2ebf-4d48-8669-0ea69d973353\\":\\"Count of records\\"}"}\n  layers={lens_xy_layer layerId="3b7791e9-326e-40d5-a787-b7594e48d906" hide=false xAccessor="77d8383e-f66e-471e-ae50-c427feedb5ba" yScaleType="linear" xScaleType="ordinal" isHistogram=false   seriesType="bar" accessors="a5c1b82d-51de-4448-a99d-6391432c3a03" columnToLabel="{\\"a5c1b82d-51de-4448-a99d-6391432c3a03\\":\\"Count of records [1]\\"}"}',
+        state: {
+          datasourceMetaData: {
+            filterableIndexPatterns: [
+              { id: '90943e30-9a47-11e8-b64d-95841ca0b247', title: 'kibana_sample_data_logs' },
+              { id: 'ff959d40-b880-11e8-a6d9-e546fe2bba5f', title: 'kibana_sample_data_ecommerce' },
+            ],
+          },
+          datasourceStates: {
+            indexpattern: {
+              currentIndexPatternId: 'ff959d40-b880-11e8-a6d9-e546fe2bba5f',
+              layers: {
+                '3b7791e9-326e-40d5-a787-b7594e48d906': {
+                  columnOrder: [
+                    '77d8383e-f66e-471e-ae50-c427feedb5ba',
+                    'a5c1b82d-51de-4448-a99d-6391432c3a03',
+                  ],
+                  columns: {
+                    '77d8383e-f66e-471e-ae50-c427feedb5ba': {
+                      dataType: 'string',
+                      isBucketed: true,
+                      label: 'Top values of geoip.country_iso_code',
+                      operationType: 'terms',
+                      params: {
+                        orderBy: {
+                          columnId: 'a5c1b82d-51de-4448-a99d-6391432c3a03',
+                          type: 'column',
+                        },
+                        orderDirection: 'desc',
+                        size: 5,
+                      },
+                      scale: 'ordinal',
+                      sourceField: 'geoip.country_iso_code',
+                    },
+                    'a5c1b82d-51de-4448-a99d-6391432c3a03': {
+                      dataType: 'number',
+                      isBucketed: false,
+                      label: 'Count of records',
+                      operationType: 'count',
+                      scale: 'ratio',
+                      sourceField: 'Records',
+                    },
+                  },
+                  indexPatternId: 'ff959d40-b880-11e8-a6d9-e546fe2bba5f',
+                },
+                '9a27f85d-35a9-4246-81b2-48e7ee9b0707': {
+                  columnOrder: [
+                    '96352896-c508-4fca-90d8-66e9ebfce621',
+                    '4ce9b4c7-2ebf-4d48-8669-0ea69d973353',
+                  ],
+                  columns: {
+                    '4ce9b4c7-2ebf-4d48-8669-0ea69d973353': {
+                      dataType: 'number',
+                      isBucketed: false,
+                      label: 'Count of records',
+                      operationType: 'count',
+                      scale: 'ratio',
+                      sourceField: 'Records',
+                    },
+                    '96352896-c508-4fca-90d8-66e9ebfce621': {
+                      dataType: 'string',
+                      isBucketed: true,
+                      label: 'Top values of geo.src',
+                      operationType: 'terms',
+                      params: {
+                        orderBy: {
+                          columnId: '4ce9b4c7-2ebf-4d48-8669-0ea69d973353',
+                          type: 'column',
+                        },
+                        orderDirection: 'desc',
+                        size: 5,
+                      },
+                      scale: 'ordinal',
+                      sourceField: 'geo.src',
+                    },
+                  },
+                  indexPatternId: '90943e30-9a47-11e8-b64d-95841ca0b247',
+                },
+              },
+            },
+          },
+          filters: [
+            {
+              $state: { store: 'appState' },
+              meta: {
+                alias: null,
+                disabled: false,
+                index: '90943e30-9a47-11e8-b64d-95841ca0b247',
+                key: 'geo.src',
+                negate: true,
+                params: { query: 'CN' },
+                type: 'phrase',
+              },
+              query: { match_phrase: { 'geo.src': 'CN' } },
+            },
+            {
+              $state: { store: 'appState' },
+              meta: {
+                alias: null,
+                disabled: false,
+                index: 'ff959d40-b880-11e8-a6d9-e546fe2bba5f',
+                key: 'geoip.country_iso_code',
+                negate: true,
+                params: { query: 'US' },
+                type: 'phrase',
+              },
+              query: { match_phrase: { 'geoip.country_iso_code': 'US' } },
+            },
+          ],
+          query: { language: 'kuery', query: 'NOT bytes > 5000' },
+          visualization: {
+            fittingFunction: 'None',
+            layers: [
+              {
+                accessors: ['4ce9b4c7-2ebf-4d48-8669-0ea69d973353'],
+                layerId: '9a27f85d-35a9-4246-81b2-48e7ee9b0707',
+                position: 'top',
+                seriesType: 'bar',
+                showGridlines: false,
+                xAccessor: '96352896-c508-4fca-90d8-66e9ebfce621',
+              },
+              {
+                accessors: ['a5c1b82d-51de-4448-a99d-6391432c3a03'],
+                layerId: '3b7791e9-326e-40d5-a787-b7594e48d906',
+                seriesType: 'bar',
+                xAccessor: '77d8383e-f66e-471e-ae50-c427feedb5ba',
+              },
+            ],
+            legend: { isVisible: true, position: 'right' },
+            preferredSeriesType: 'bar',
+          },
+        },
+        title: 'mylens',
+        visualizationType: 'lnsXY',
+      },
+      type: 'lens',
+    };
+
+    it('should remove expression', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(result.attributes.expression).toBeUndefined();
+    });
+
+    it('should list references for layers', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(
+        result.references?.find(
+          (ref) => ref.name === 'indexpattern-datasource-layer-3b7791e9-326e-40d5-a787-b7594e48d906'
+        )?.id
+      ).toEqual('ff959d40-b880-11e8-a6d9-e546fe2bba5f');
+      expect(
+        result.references?.find(
+          (ref) => ref.name === 'indexpattern-datasource-layer-9a27f85d-35a9-4246-81b2-48e7ee9b0707'
+        )?.id
+      ).toEqual('90943e30-9a47-11e8-b64d-95841ca0b247');
+    });
+
+    it('should remove index pattern ids from layers', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(
+        result.attributes.state.datasourceStates.indexpattern.layers[
+          '3b7791e9-326e-40d5-a787-b7594e48d906'
+        ].indexPatternId
+      ).toBeUndefined();
+      expect(
+        result.attributes.state.datasourceStates.indexpattern.layers[
+          '9a27f85d-35a9-4246-81b2-48e7ee9b0707'
+        ].indexPatternId
+      ).toBeUndefined();
+    });
+
+    it('should remove datsource meta data', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(result.attributes.state.datasourceMetaData).toBeUndefined();
+    });
+
+    it('should list references for filters', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(result.references?.find((ref) => ref.name === 'filter-index-pattern-0')?.id).toEqual(
+        '90943e30-9a47-11e8-b64d-95841ca0b247'
+      );
+      expect(result.references?.find((ref) => ref.name === 'filter-index-pattern-1')?.id).toEqual(
+        'ff959d40-b880-11e8-a6d9-e546fe2bba5f'
+      );
+    });
+
+    it('should remove index pattern ids from filters', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(result.attributes.state.filters[0].meta.index).toBeUndefined();
+      expect(result.attributes.state.filters[0].meta.indexRefName).toEqual(
+        'filter-index-pattern-0'
+      );
+      expect(result.attributes.state.filters[1].meta.index).toBeUndefined();
+      expect(result.attributes.state.filters[1].meta.indexRefName).toEqual(
+        'filter-index-pattern-1'
+      );
+    });
+
+    it('should list reference for current index pattern', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(
+        result.references?.find(
+          (ref) => ref.name === 'indexpattern-datasource-current-indexpattern'
+        )?.id
+      ).toEqual('ff959d40-b880-11e8-a6d9-e546fe2bba5f');
+    });
+
+    it('should remove current index pattern id from datasource state', () => {
+      const result = migrations['7.10.0'](example, context);
+      expect(
+        result.attributes.state.datasourceStates.indexpattern.currentIndexPatternId
+      ).toBeUndefined();
+    });
+
+    it('should produce a valid document', () => {
+      const result = migrations['7.10.0'](example, context);
+      // changes to the outcome of this are critical - this test is a safe guard to not introduce changes accidentally
+      // if this test fails, make extra sure it's expected
+      expect(result).toMatchSnapshot();
+    });
+  });
 });
diff --git a/x-pack/plugins/lens/server/migrations.ts b/x-pack/plugins/lens/server/migrations.ts
index d24a3e92cbd9c..fdbfa1e455f60 100644
--- a/x-pack/plugins/lens/server/migrations.ts
+++ b/x-pack/plugins/lens/server/migrations.ts
@@ -6,11 +6,16 @@
 
 import { cloneDeep } from 'lodash';
 import { fromExpression, toExpression, Ast, ExpressionFunctionAST } from '@kbn/interpreter/common';
-import { SavedObjectMigrationMap, SavedObjectMigrationFn } from 'src/core/server';
+import {
+  SavedObjectMigrationMap,
+  SavedObjectMigrationFn,
+  SavedObjectReference,
+  SavedObjectUnsanitizedDoc,
+} from 'src/core/server';
+import { Query, Filter } from 'src/plugins/data/public';
+import { PersistableFilter } from '../common';
 
-interface LensDocShape<VisualizationState = unknown> {
-  id?: string;
-  type?: string;
+interface LensDocShapePre710<VisualizationState = unknown> {
   visualizationType: string | null;
   title: string;
   expression: string | null;
@@ -21,18 +26,44 @@ interface LensDocShape<VisualizationState = unknown> {
     datasourceStates: {
       // This is hardcoded as our only datasource
       indexpattern: {
+        currentIndexPatternId: string;
         layers: Record<
           string,
           {
             columnOrder: string[];
             columns: Record<string, unknown>;
+            indexPatternId: string;
           }
         >;
       };
     };
     visualization: VisualizationState;
-    query: unknown;
-    filters: unknown[];
+    query: Query;
+    filters: Filter[];
+  };
+}
+
+interface LensDocShape<VisualizationState = unknown> {
+  id?: string;
+  type?: string;
+  visualizationType: string | null;
+  title: string;
+  state: {
+    datasourceStates: {
+      // This is hardcoded as our only datasource
+      indexpattern: {
+        layers: Record<
+          string,
+          {
+            columnOrder: string[];
+            columns: Record<string, unknown>;
+          }
+        >;
+      };
+    };
+    visualization: VisualizationState;
+    query: Query;
+    filters: PersistableFilter[];
   };
 }
 
@@ -55,7 +86,10 @@ interface XYStatePost77 {
  * Removes the `lens_auto_date` subexpression from a stored expression
  * string. For example: aggConfigs={lens_auto_date aggConfigs="JSON string"}
  */
-const removeLensAutoDate: SavedObjectMigrationFn<LensDocShape, LensDocShape> = (doc, context) => {
+const removeLensAutoDate: SavedObjectMigrationFn<LensDocShapePre710, LensDocShapePre710> = (
+  doc,
+  context
+) => {
   const expression = doc.attributes.expression;
   if (!expression) {
     return doc;
@@ -112,7 +146,10 @@ const removeLensAutoDate: SavedObjectMigrationFn<LensDocShape, LensDocShape> = (
 /**
  * Adds missing timeField arguments to esaggs in the Lens expression
  */
-const addTimeFieldToEsaggs: SavedObjectMigrationFn<LensDocShape, LensDocShape> = (doc, context) => {
+const addTimeFieldToEsaggs: SavedObjectMigrationFn<LensDocShapePre710, LensDocShapePre710> = (
+  doc,
+  context
+) => {
   const expression = doc.attributes.expression;
   if (!expression) {
     return doc;
@@ -174,14 +211,14 @@ const addTimeFieldToEsaggs: SavedObjectMigrationFn<LensDocShape, LensDocShape> =
 };
 
 const removeInvalidAccessors: SavedObjectMigrationFn<
-  LensDocShape<XYStatePre77>,
-  LensDocShape<XYStatePost77>
+  LensDocShapePre710<XYStatePre77>,
+  LensDocShapePre710<XYStatePost77>
 > = (doc) => {
   const newDoc = cloneDeep(doc);
   if (newDoc.attributes.visualizationType === 'lnsXY') {
     const datasourceLayers = newDoc.attributes.state.datasourceStates.indexpattern.layers || {};
     const xyState = newDoc.attributes.state.visualization;
-    (newDoc.attributes as LensDocShape<
+    (newDoc.attributes as LensDocShapePre710<
       XYStatePost77
     >).state.visualization.layers = xyState.layers.map((layer: XYLayerPre77) => {
       const layerId = layer.layerId;
@@ -197,9 +234,86 @@ const removeInvalidAccessors: SavedObjectMigrationFn<
   return newDoc;
 };
 
+const extractReferences: SavedObjectMigrationFn<LensDocShapePre710, LensDocShape> = ({
+  attributes,
+  references,
+  ...docMeta
+}) => {
+  const savedObjectReferences: SavedObjectReference[] = [];
+  // add currently selected index pattern to reference list
+  savedObjectReferences.push({
+    type: 'index-pattern',
+    id: attributes.state.datasourceStates.indexpattern.currentIndexPatternId,
+    name: 'indexpattern-datasource-current-indexpattern',
+  });
+
+  // add layer index patterns to list and remove index pattern ids from layers
+  const persistableLayers: Record<
+    string,
+    Omit<
+      LensDocShapePre710['state']['datasourceStates']['indexpattern']['layers'][string],
+      'indexPatternId'
+    >
+  > = {};
+  Object.entries(attributes.state.datasourceStates.indexpattern.layers).forEach(
+    ([layerId, { indexPatternId, ...persistableLayer }]) => {
+      savedObjectReferences.push({
+        type: 'index-pattern',
+        id: indexPatternId,
+        name: `indexpattern-datasource-layer-${layerId}`,
+      });
+      persistableLayers[layerId] = persistableLayer;
+    }
+  );
+
+  // add filter index patterns to reference list and remove index pattern ids from filter definitions
+  const persistableFilters = attributes.state.filters.map((filterRow, i) => {
+    if (!filterRow.meta || !filterRow.meta.index) {
+      return filterRow;
+    }
+    const refName = `filter-index-pattern-${i}`;
+    savedObjectReferences.push({
+      name: refName,
+      type: 'index-pattern',
+      id: filterRow.meta.index,
+    });
+    return {
+      ...filterRow,
+      meta: {
+        ...filterRow.meta,
+        indexRefName: refName,
+        index: undefined,
+      },
+    };
+  });
+
+  // put together new saved object format
+  const newDoc: SavedObjectUnsanitizedDoc<LensDocShape> = {
+    ...docMeta,
+    references: savedObjectReferences,
+    attributes: {
+      visualizationType: attributes.visualizationType,
+      title: attributes.title,
+      state: {
+        datasourceStates: {
+          indexpattern: {
+            layers: persistableLayers,
+          },
+        },
+        visualization: attributes.state.visualization,
+        query: attributes.state.query,
+        filters: persistableFilters,
+      },
+    },
+  };
+
+  return newDoc;
+};
+
 export const migrations: SavedObjectMigrationMap = {
   '7.7.0': removeInvalidAccessors,
   // The order of these migrations matter, since the timefield migration relies on the aggConfigs
   // sitting directly on the esaggs as an argument and not a nested function (which lens_auto_date was).
   '7.8.0': (doc, context) => addTimeFieldToEsaggs(removeLensAutoDate(doc, context), context),
+  '7.10.0': extractReferences,
 };