diff --git a/src/plugins/data/public/query/state_sync/connect_to_query_state.test.ts b/src/plugins/data/public/query/state_sync/connect_to_query_state.test.ts
index 5da929c441cde..06e4c1c8be6d5 100644
--- a/src/plugins/data/public/query/state_sync/connect_to_query_state.test.ts
+++ b/src/plugins/data/public/query/state_sync/connect_to_query_state.test.ts
@@ -463,3 +463,97 @@ describe('connect_to_app_state', () => {
     });
   });
 });
+
+describe('filters with different state', () => {
+  let queryServiceStart: QueryStart;
+  let filterManager: FilterManager;
+  let state: BaseStateContainer<QueryState>;
+  let stateSub: Subscription;
+  let stateChangeTriggered = jest.fn();
+  let filterManagerChangeSub: Subscription;
+  let filterManagerChangeTriggered = jest.fn();
+
+  let filter: Filter;
+
+  beforeEach(() => {
+    const queryService = new QueryService();
+    queryService.setup({
+      uiSettings: setupMock.uiSettings,
+      storage: new Storage(new StubBrowserStorage()),
+    });
+    queryServiceStart = queryService.start(startMock.savedObjects);
+    filterManager = queryServiceStart.filterManager;
+
+    state = createStateContainer({});
+    stateChangeTriggered = jest.fn();
+    stateSub = state.state$.subscribe(stateChangeTriggered);
+
+    filterManagerChangeTriggered = jest.fn();
+    filterManagerChangeSub = filterManager.getUpdates$().subscribe(filterManagerChangeTriggered);
+
+    filter = getFilter(FilterStateStore.GLOBAL_STATE, true, true, 'key1', 'value1');
+  });
+
+  // applies filter state changes, changes only internal $state.store value
+  function runChanges() {
+    filter = { ...filter, $state: { store: FilterStateStore.GLOBAL_STATE } };
+
+    state.set({
+      filters: [filter],
+    });
+
+    filter = { ...filter, $state: { store: FilterStateStore.APP_STATE } };
+
+    state.set({
+      filters: [filter],
+    });
+
+    filter = { ...filter };
+    delete filter.$state;
+
+    state.set({
+      filters: [filter],
+    });
+  }
+
+  test('when syncing all filters, changes to filter.state$ should be taken into account', () => {
+    const stop = connectToQueryState(queryServiceStart, state, {
+      filters: true,
+    });
+
+    runChanges();
+
+    expect(filterManagerChangeTriggered).toBeCalledTimes(3);
+
+    stop();
+  });
+
+  test('when syncing app state filters, changes to filter.state$ should be ignored', () => {
+    const stop = connectToQueryState(queryServiceStart, state, {
+      filters: FilterStateStore.APP_STATE,
+    });
+
+    runChanges();
+
+    expect(filterManagerChangeTriggered).toBeCalledTimes(1);
+
+    stop();
+  });
+
+  test('when syncing global state filters, changes to filter.state$ should be ignored', () => {
+    const stop = connectToQueryState(queryServiceStart, state, {
+      filters: FilterStateStore.GLOBAL_STATE,
+    });
+
+    runChanges();
+
+    expect(filterManagerChangeTriggered).toBeCalledTimes(1);
+
+    stop();
+  });
+
+  afterEach(() => {
+    stateSub.unsubscribe();
+    filterManagerChangeSub.unsubscribe();
+  });
+});
diff --git a/src/plugins/data/public/query/state_sync/connect_to_query_state.ts b/src/plugins/data/public/query/state_sync/connect_to_query_state.ts
index 331d8969f2483..3256c1cbd65a1 100644
--- a/src/plugins/data/public/query/state_sync/connect_to_query_state.ts
+++ b/src/plugins/data/public/query/state_sync/connect_to_query_state.ts
@@ -91,7 +91,10 @@ export const connectToQueryState = <S extends QueryState>(
     } else if (syncConfig.filters === FilterStateStore.GLOBAL_STATE) {
       if (
         !initialState.filters ||
-        !compareFilters(initialState.filters, filterManager.getGlobalFilters(), COMPARE_ALL_OPTIONS)
+        !compareFilters(initialState.filters, filterManager.getGlobalFilters(), {
+          ...COMPARE_ALL_OPTIONS,
+          state: false,
+        })
       ) {
         initialState.filters = filterManager.getGlobalFilters();
         initialDirty = true;
@@ -99,7 +102,10 @@ export const connectToQueryState = <S extends QueryState>(
     } else if (syncConfig.filters === FilterStateStore.APP_STATE) {
       if (
         !initialState.filters ||
-        !compareFilters(initialState.filters, filterManager.getAppFilters(), COMPARE_ALL_OPTIONS)
+        !compareFilters(initialState.filters, filterManager.getAppFilters(), {
+          ...COMPARE_ALL_OPTIONS,
+          state: false,
+        })
       ) {
         initialState.filters = filterManager.getAppFilters();
         initialDirty = true;
@@ -173,11 +179,21 @@ export const connectToQueryState = <S extends QueryState>(
             filterManager.setFilters(_.cloneDeep(filters));
           }
         } else if (syncConfig.filters === FilterStateStore.APP_STATE) {
-          if (!compareFilters(filters, filterManager.getAppFilters(), COMPARE_ALL_OPTIONS)) {
+          if (
+            !compareFilters(filters, filterManager.getAppFilters(), {
+              ...COMPARE_ALL_OPTIONS,
+              state: false,
+            })
+          ) {
             filterManager.setAppFilters(_.cloneDeep(filters));
           }
         } else if (syncConfig.filters === FilterStateStore.GLOBAL_STATE) {
-          if (!compareFilters(filters, filterManager.getGlobalFilters(), COMPARE_ALL_OPTIONS)) {
+          if (
+            !compareFilters(filters, filterManager.getGlobalFilters(), {
+              ...COMPARE_ALL_OPTIONS,
+              state: false,
+            })
+          ) {
             filterManager.setGlobalFilters(_.cloneDeep(filters));
           }
         }