diff --git a/code/lib/manager-api/src/modules/stories.ts b/code/lib/manager-api/src/modules/stories.ts
index 78c3307f179f..19ea80ce41f4 100644
--- a/code/lib/manager-api/src/modules/stories.ts
+++ b/code/lib/manager-api/src/modules/stories.ts
@@ -648,17 +648,20 @@ export const init: ModuleFn<SubAPI, SubState> = ({
       }
     },
     experimental_setFilter: async (id, filterFunction) => {
-      const { internal_index: index } = store.getState();
       await store.setState({ filters: { ...store.getState().filters, [id]: filterFunction } });
 
-      if (index) {
-        await api.setIndex(index);
+      const { internal_index: index } = store.getState();
 
-        const refs = await fullAPI.getRefs();
-        Object.entries(refs).forEach(([refId, { internal_index, ...ref }]) => {
-          fullAPI.setRef(refId, { ...ref, storyIndex: internal_index }, true);
-        });
+      if (!index) {
+        return;
       }
+      // apply new filters by setting the index again
+      await api.setIndex(index);
+
+      const refs = await fullAPI.getRefs();
+      Object.entries(refs).forEach(([refId, { internal_index, ...ref }]) => {
+        fullAPI.setRef(refId, { ...ref, storyIndex: internal_index }, true);
+      });
     },
   };
 
@@ -879,6 +882,7 @@ export const init: ModuleFn<SubAPI, SubState> = ({
     },
     init: async () => {
       provider.channel?.on(STORY_INDEX_INVALIDATED, () => api.fetchIndex());
+
       await api.fetchIndex();
     },
   };