diff --git a/src/plugins/data/public/actions/filters/create_filters_from_value_click.test.ts b/src/plugins/data/public/actions/filters/create_filters_from_value_click.test.ts
index 30667d59eff84..14ae24a2a5626 100644
--- a/src/plugins/data/public/actions/filters/create_filters_from_value_click.test.ts
+++ b/src/plugins/data/public/actions/filters/create_filters_from_value_click.test.ts
@@ -105,4 +105,11 @@ describe('createFiltersFromValueClick', () => {
       expect(rangeFilter.range.bytes.lt).toEqual(2078);
     }
   });
+
+  test('handles non-unique filters', async () => {
+    const [point] = dataPoints;
+    const filters = await createFiltersFromValueClickAction({ data: [point, point] });
+
+    expect(filters.length).toEqual(1);
+  });
 });
diff --git a/src/plugins/data/public/actions/filters/create_filters_from_value_click.ts b/src/plugins/data/public/actions/filters/create_filters_from_value_click.ts
index fb8240a0cdc27..13cb9ba419bf9 100644
--- a/src/plugins/data/public/actions/filters/create_filters_from_value_click.ts
+++ b/src/plugins/data/public/actions/filters/create_filters_from_value_click.ts
@@ -6,6 +6,7 @@
  * Side Public License, v 1.
  */
 
+import _ from 'lodash';
 import { Datatable } from '../../../../../plugins/expressions/public';
 import { esFilters, Filter } from '../../../public';
 import { getIndexPatterns, getSearchService } from '../../../public/services';
@@ -140,5 +141,7 @@ export const createFiltersFromValueClickAction = async ({
       })
   );
 
-  return esFilters.mapAndFlattenFilters(filters);
+  return _.uniqWith(esFilters.mapAndFlattenFilters(filters), (a, b) =>
+    esFilters.compareFilters(a, b, esFilters.COMPARE_ALL_OPTIONS)
+  );
 };
diff --git a/src/plugins/data/public/query/filter_manager/lib/generate_filter.test.ts b/src/plugins/data/public/query/filter_manager/lib/generate_filter.test.ts
index 1a29a57ff058a..0daaf804e7b40 100644
--- a/src/plugins/data/public/query/filter_manager/lib/generate_filter.test.ts
+++ b/src/plugins/data/public/query/filter_manager/lib/generate_filter.test.ts
@@ -174,4 +174,22 @@ describe('Generate filters', () => {
       [FIELD.name]: ANOTHER_PHRASE,
     });
   });
+
+  it('should use only distinct values', () => {
+    const ANOTHER_PHRASE = 'another-value';
+    const filters = generateFilters(
+      mockFilterManager,
+      FIELD,
+      [PHRASE_VALUE, ANOTHER_PHRASE, PHRASE_VALUE, ANOTHER_PHRASE],
+      '',
+      INDEX_NAME
+    );
+    expect(filters).toHaveLength(2);
+    expect((filters[0] as PhraseFilter).query.match_phrase).toEqual({
+      [FIELD.name]: PHRASE_VALUE,
+    });
+    expect((filters[1] as PhraseFilter).query.match_phrase).toEqual({
+      [FIELD.name]: ANOTHER_PHRASE,
+    });
+  });
 });
diff --git a/src/plugins/data/public/query/filter_manager/lib/generate_filters.ts b/src/plugins/data/public/query/filter_manager/lib/generate_filters.ts
index 9a52a02edcd4e..0a4998a159523 100644
--- a/src/plugins/data/public/query/filter_manager/lib/generate_filters.ts
+++ b/src/plugins/data/public/query/filter_manager/lib/generate_filters.ts
@@ -71,7 +71,7 @@ export function generateFilters(
   operation: string,
   index: string
 ): Filter[] {
-  values = Array.isArray(values) ? values : [values];
+  values = Array.isArray(values) ? _.uniq(values) : [values];
   const fieldObj = (_.isObject(field)
     ? field
     : {