diff --git a/x-pack/legacy/plugins/lens/public/app_plugin/app.test.tsx b/x-pack/legacy/plugins/lens/public/app_plugin/app.test.tsx
index 794128832461ba..80a7ceb61c324c 100644
--- a/x-pack/legacy/plugins/lens/public/app_plugin/app.test.tsx
+++ b/x-pack/legacy/plugins/lens/public/app_plugin/app.test.tsx
@@ -12,7 +12,12 @@ import { EditorFrameInstance } from '../types';
 import { Storage } from '../../../../../../src/plugins/kibana_utils/public';
 import { Document, SavedObjectStore } from '../persistence';
 import { mount } from 'enzyme';
-import { esFilters, IFieldType, IIndexPattern } from '../../../../../../src/plugins/data/public';
+import {
+  esFilters,
+  FilterManager,
+  IFieldType,
+  IIndexPattern,
+} from '../../../../../../src/plugins/data/public';
 import { dataPluginMock } from '../../../../../../src/plugins/data/public/mocks';
 const dataStartMock = dataPluginMock.createStartContract();
 
@@ -60,6 +65,10 @@ function createMockFilterManager() {
       subscriber();
     },
     getFilters: () => filters,
+    getGlobalFilters: () => {
+      // @ts-ignore
+      return filters.filter(esFilters.isFilterPinned);
+    },
     removeAll: () => {
       filters = [];
       subscriber();
@@ -821,7 +830,7 @@ describe('Lens App', () => {
       );
     });
 
-    it('clears all existing filters when the active saved query is cleared', () => {
+    it('clears all existing unpinned filters when the active saved query is cleared', () => {
       const args = makeDefaultArgs();
       args.editorFrame = frame;
 
@@ -834,8 +843,13 @@ describe('Lens App', () => {
 
       const indexPattern = ({ id: 'index1' } as unknown) as IIndexPattern;
       const field = ({ name: 'myfield' } as unknown) as IFieldType;
+      const pinnedField = ({ name: 'pinnedField' } as unknown) as IFieldType;
 
-      args.data.query.filterManager.setFilters([esFilters.buildExistsFilter(field, indexPattern)]);
+      const unpinned = esFilters.buildExistsFilter(field, indexPattern);
+      const pinned = esFilters.buildExistsFilter(pinnedField, indexPattern);
+      FilterManager.setFiltersStore([pinned], esFilters.FilterStateStore.GLOBAL_STATE);
+
+      args.data.query.filterManager.setFilters([pinned, unpinned]);
       instance.update();
 
       instance.find(TopNavMenu).prop('onClearSavedQuery')!();
@@ -844,7 +858,7 @@ describe('Lens App', () => {
       expect(frame.mount).toHaveBeenLastCalledWith(
         expect.any(Element),
         expect.objectContaining({
-          filters: [],
+          filters: [pinned],
         })
       );
     });
diff --git a/x-pack/legacy/plugins/lens/public/app_plugin/app.tsx b/x-pack/legacy/plugins/lens/public/app_plugin/app.tsx
index 615e91f56df6c5..35e45af6a3d689 100644
--- a/x-pack/legacy/plugins/lens/public/app_plugin/app.tsx
+++ b/x-pack/legacy/plugins/lens/public/app_plugin/app.tsx
@@ -258,7 +258,7 @@ export function App({
                 setState(s => ({
                   ...s,
                   savedQuery: undefined,
-                  filters: [],
+                  filters: data.query.filterManager.getGlobalFilters(),
                   query: {
                     query: '',
                     language: