diff --git a/superset-frontend/src/dashboard/components/FiltersBadge/index.tsx b/superset-frontend/src/dashboard/components/FiltersBadge/index.tsx
index aad602403369..c9ed50785f3c 100644
--- a/superset-frontend/src/dashboard/components/FiltersBadge/index.tsx
+++ b/superset-frontend/src/dashboard/components/FiltersBadge/index.tsx
@@ -201,30 +201,37 @@ export const FiltersBadge = ({ chartId }: FiltersBadgeProps) => {
   const prevChartConfig = usePrevious(chartConfiguration);
 
   useEffect(() => {
-    if (!showIndicators && nativeIndicators.length > 0) {
+    const shouldReset =
+      (!chart ||
+        chart.chartStatus === 'failed' ||
+        chart.chartStatus === null) &&
+      nativeIndicators.length > 0;
+
+    const shouldRecalculate =
+      chart?.queriesResponse?.[0]?.rejected_filters !==
+        prevChart?.queriesResponse?.[0]?.rejected_filters ||
+      chart?.queriesResponse?.[0]?.applied_filters !==
+        prevChart?.queriesResponse?.[0]?.applied_filters ||
+      nativeFilters !== prevNativeFilters ||
+      chartLayoutItems !== prevChartLayoutItems ||
+      dataMask !== prevDataMask ||
+      prevChartConfig !== chartConfiguration;
+
+    if (shouldReset) {
       setNativeIndicators(indicatorsInitialState);
-    } else if (prevChartStatus !== 'success') {
-      if (
-        chart?.queriesResponse?.[0]?.rejected_filters !==
-          prevChart?.queriesResponse?.[0]?.rejected_filters ||
-        chart?.queriesResponse?.[0]?.applied_filters !==
-          prevChart?.queriesResponse?.[0]?.applied_filters ||
-        nativeFilters !== prevNativeFilters ||
-        chartLayoutItems !== prevChartLayoutItems ||
-        dataMask !== prevDataMask ||
-        prevChartConfig !== chartConfiguration
-      ) {
-        setNativeIndicators(
-          selectNativeIndicatorsForChart(
-            nativeFilters,
-            dataMask,
-            chartId,
-            chart,
-            chartLayoutItems,
-            chartConfiguration,
-          ),
-        );
-      }
+    } else if (
+      showIndicators &&
+      (shouldRecalculate || nativeIndicators.length === 0)
+    ) {
+      const newIndicators = selectNativeIndicatorsForChart(
+        nativeFilters,
+        dataMask,
+        chartId,
+        chart,
+        chartLayoutItems,
+        chartConfiguration,
+      );
+      setNativeIndicators(newIndicators);
     }
   }, [
     chart,
diff --git a/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/FilterBar.test.tsx b/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/FilterBar.test.tsx
index 96e2770603ef..17ed9cba224b 100644
--- a/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/FilterBar.test.tsx
+++ b/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/FilterBar.test.tsx
@@ -27,6 +27,7 @@ import { FilterBarOrientation } from 'src/dashboard/types';
 import { FILTER_BAR_TEST_ID } from './utils';
 import FilterBar from '.';
 import { FILTERS_CONFIG_MODAL_TEST_ID } from '../FiltersConfigModal/FiltersConfigModal';
+import * as dataMaskActions from 'src/dataMask/actions';
 
 jest.useFakeTimers();
 
@@ -350,4 +351,118 @@ describe('FilterBar', () => {
     const { container } = renderWrapper(openedBarProps, stateWithFilter);
     expect(container).toBeInTheDocument();
   });
+
+  test('auto-applies filter when extraFormData is empty in applied state', async () => {
+    const filterId = 'test-filter-auto-apply';
+    const updateDataMaskSpy = jest.spyOn(dataMaskActions, 'updateDataMask');
+
+    const stateWithIncompleteFilter = {
+      ...stateWithoutNativeFilters,
+      dashboardInfo: {
+        id: 1,
+        dash_edit_perm: true,
+      },
+      dataMask: {
+        [filterId]: {
+          id: filterId,
+          filterState: { value: ['value1', 'value2'] },
+          extraFormData: {},
+        },
+      },
+      nativeFilters: {
+        filters: {
+          [filterId]: {
+            id: filterId,
+            name: 'Test Filter',
+            filterType: 'filter_select',
+            targets: [{ datasetId: 1, column: { name: 'test_column' } }],
+            defaultDataMask: {
+              filterState: { value: ['value1', 'value2'] },
+              extraFormData: {},
+            },
+            controlValues: {
+              enableEmptyFilter: true,
+            },
+            cascadeParentIds: [],
+            scope: {
+              rootPath: ['ROOT_ID'],
+              excluded: [],
+            },
+            type: 'NATIVE_FILTER',
+            description: '',
+            chartsInScope: [],
+            tabsInScope: [],
+          },
+        },
+        filtersState: {},
+      },
+    };
+
+    renderWrapper(openedBarProps, stateWithIncompleteFilter);
+
+    await act(async () => {
+      jest.advanceTimersByTime(200);
+    });
+
+    expect(screen.getByTestId(getTestId('filter-icon'))).toBeInTheDocument();
+
+    updateDataMaskSpy.mockRestore();
+  });
+
+  test('renders correctly when filter has complete extraFormData', async () => {
+    const filterId = 'test-filter-complete';
+    const stateWithCompleteFilter = {
+      ...stateWithoutNativeFilters,
+      dashboardInfo: {
+        id: 1,
+        dash_edit_perm: true,
+      },
+      dataMask: {
+        [filterId]: {
+          id: filterId,
+          filterState: { value: ['value1'] },
+          extraFormData: {
+            filters: [{ col: 'test_column', op: 'IN', val: ['value1'] }],
+          },
+        },
+      },
+      nativeFilters: {
+        filters: {
+          [filterId]: {
+            id: filterId,
+            name: 'Test Filter',
+            filterType: 'filter_select',
+            targets: [{ datasetId: 1, column: { name: 'test_column' } }],
+            defaultDataMask: {
+              filterState: { value: ['value1'] },
+              extraFormData: {
+                filters: [{ col: 'test_column', op: 'IN', val: ['value1'] }],
+              },
+            },
+            controlValues: {
+              enableEmptyFilter: true,
+            },
+            cascadeParentIds: [],
+            scope: {
+              rootPath: ['ROOT_ID'],
+              excluded: [],
+            },
+            type: 'NATIVE_FILTER',
+            description: '',
+            chartsInScope: [],
+            tabsInScope: [],
+          },
+        },
+        filtersState: {},
+      },
+    };
+
+    renderWrapper(openedBarProps, stateWithCompleteFilter);
+
+    await act(async () => {
+      jest.advanceTimersByTime(100);
+    });
+
+    expect(screen.getByTestId(getTestId('filter-icon'))).toBeInTheDocument();
+  });
 });
diff --git a/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/index.tsx b/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/index.tsx
index 74d90cbb9926..d7f787254ba9 100644
--- a/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/index.tsx
+++ b/superset-frontend/src/dashboard/components/nativeFilters/FilterBar/index.tsx
@@ -204,24 +204,41 @@ const FilterBar: FC<FiltersBarProps> = ({
       dataMask: Partial<DataMask>,
     ) => {
       setDataMaskSelected(draft => {
-        const isFirstTimeInitialization =
-          !initializedFilters.has(filter.id) &&
-          dataMaskSelectedRef.current[filter.id]?.filterState?.value ===
-            undefined;
-
-        // force instant updating on initialization for filters with `requiredFirst` is true or instant filters
-        if (
-          // filterState.value === undefined - means that value not initialized
+        const appliedDataMask = dataMaskApplied[filter.id];
+        const isFirstTimeInitialization = !initializedFilters.has(filter.id);
+
+        // Auto-apply when filter has value but empty extraFormData in applied state
+        // This fixes the bug where defaultDataMask.filterState.value exists but extraFormData is empty
+        // Only auto-apply if: value matches what's applied AND extraFormData is missing in applied but present in incoming
+        const needsAutoApply =
+          appliedDataMask?.filterState?.value !== undefined &&
           dataMask.filterState?.value !== undefined &&
-          isFirstTimeInitialization &&
-          filter.requiredFirst
-        ) {
+          isEqual(
+            appliedDataMask.filterState.value,
+            dataMask.filterState.value,
+          ) &&
+          (!appliedDataMask?.extraFormData ||
+            Object.keys(appliedDataMask.extraFormData || {}).length === 0) &&
+          dataMask.extraFormData &&
+          Object.keys(dataMask.extraFormData).length > 0;
+
+        // Force instant updating for requiredFirst filters or auto-apply when needed
+        const shouldDispatch =
+          dataMask.filterState?.value !== undefined &&
+          ((isFirstTimeInitialization && filter.requiredFirst) ||
+            needsAutoApply);
+
+        if (shouldDispatch) {
           dispatch(updateDataMask(filter.id, dataMask));
         }
 
-        // Mark filter as initialized after getting its first value
+        // Mark filter as initialized after getting its first value WITH extraFormData
+        // This ensures we don't mark it as initialized on the first sync (value but no extraFormData)
+        // but do mark it after the second sync (value AND extraFormData)
         if (
           dataMask.filterState?.value !== undefined &&
+          dataMask.extraFormData &&
+          Object.keys(dataMask.extraFormData).length > 0 &&
           !initializedFilters.has(filter.id)
         ) {
           setInitializedFilters(prev => new Set(prev).add(filter.id));
@@ -252,7 +269,13 @@ const FilterBar: FC<FiltersBarProps> = ({
         };
       });
     },
-    [dispatch, setDataMaskSelected, initializedFilters, setInitializedFilters],
+    [
+      dispatch,
+      setDataMaskSelected,
+      initializedFilters,
+      setInitializedFilters,
+      dataMaskApplied,
+    ],
   );
 
   useEffect(() => {