diff --git a/public/app/plugins/panel/geomap/utils/layers.test.ts b/public/app/plugins/panel/geomap/utils/layers.test.ts
new file mode 100644
index 00000000000..1310d892481
--- /dev/null
+++ b/public/app/plugins/panel/geomap/utils/layers.test.ts
@@ -0,0 +1,123 @@
+jest.mock('ol-mapbox-style', () => ({}));
+jest.mock('geotiff', () => ({}));
+
+import BaseLayer from 'ol/layer/Base';
+
+import {
+  DataFrame,
+  DataQueryRequest,
+  FieldType,
+  LoadingState,
+  MapLayerHandler,
+  MapLayerOptions,
+  PanelData,
+  TimeRange,
+} from '@grafana/data';
+
+import { applyLayerFilter } from './layers';
+
+describe('applyLayerFilter', () => {
+  const createDataFrame = (refId: string): DataFrame => ({
+    refId,
+    fields: [{ name: 'value', type: FieldType.number, values: [1, 2, 3], config: {} }],
+    length: 3,
+  });
+
+  it('should apply filter when query exists and is visible', () => {
+    const update = jest.fn();
+    const handler: MapLayerHandler = {
+      init: () => ({}) as BaseLayer,
+      update,
+    };
+    const options: MapLayerOptions = {
+      name: 'Test',
+      type: 'markers',
+      filterData: { id: 'byRefId', options: 'A' },
+    };
+    const panelData: PanelData = {
+      series: [createDataFrame('A'), createDataFrame('B')],
+      state: LoadingState.Done,
+      timeRange: {} as TimeRange,
+      request: { targets: [{ refId: 'A' }, { refId: 'B' }] } as DataQueryRequest,
+    };
+
+    applyLayerFilter(handler, options, panelData);
+
+    expect(update).toHaveBeenCalledWith(
+      expect.objectContaining({
+        series: [createDataFrame('A')],
+      })
+    );
+  });
+
+  it('should return empty series when query exists but is hidden', () => {
+    const update = jest.fn();
+    const handler: MapLayerHandler = {
+      init: () => ({}) as BaseLayer,
+      update,
+    };
+    const options: MapLayerOptions = {
+      name: 'Test',
+      type: 'markers',
+      filterData: { id: 'byRefId', options: 'A' },
+    };
+    const panelData: PanelData = {
+      series: [createDataFrame('B')],
+      state: LoadingState.Done,
+      timeRange: {} as TimeRange,
+      request: { targets: [{ refId: 'A', hide: true }, { refId: 'B' }] } as DataQueryRequest,
+    };
+
+    applyLayerFilter(handler, options, panelData);
+
+    expect(update).toHaveBeenCalledWith(
+      expect.objectContaining({
+        series: [],
+      })
+    );
+  });
+
+  it('should not apply filter when query does not exist', () => {
+    const update = jest.fn();
+    const handler: MapLayerHandler = {
+      init: () => ({}) as BaseLayer,
+      update,
+    };
+    const options: MapLayerOptions = {
+      name: 'Test',
+      type: 'markers',
+      filterData: { id: 'byRefId', options: 'C' },
+    };
+    const panelData: PanelData = {
+      series: [createDataFrame('A'), createDataFrame('B')],
+      state: LoadingState.Done,
+      timeRange: {} as TimeRange,
+      request: { targets: [{ refId: 'A' }, { refId: 'B' }] } as DataQueryRequest,
+    };
+
+    applyLayerFilter(handler, options, panelData);
+
+    expect(update).toHaveBeenCalledWith(panelData);
+  });
+
+  it('should pass through all data when no filter is configured', () => {
+    const update = jest.fn();
+    const handler: MapLayerHandler = {
+      init: () => ({}) as BaseLayer,
+      update,
+    };
+    const options: MapLayerOptions = {
+      name: 'Test',
+      type: 'markers',
+    };
+    const panelData: PanelData = {
+      series: [createDataFrame('A'), createDataFrame('B')],
+      state: LoadingState.Done,
+      timeRange: {} as TimeRange,
+    };
+
+    applyLayerFilter(handler, options, panelData);
+
+    expect(update).toHaveBeenCalledWith(panelData);
+  });
+});
diff --git a/public/app/plugins/panel/geomap/utils/layers.ts b/public/app/plugins/panel/geomap/utils/layers.ts
index f20d8891ade..925ec1a82c4 100644
--- a/public/app/plugins/panel/geomap/utils/layers.ts
+++ b/public/app/plugins/panel/geomap/utils/layers.ts
@@ -26,7 +26,13 @@ export const applyLayerFilter = (
     let panelData = panelDataProps;
     if (options.filterData) {
       const matcherFunc = getFrameMatchers(options.filterData);
-      if (panelData.series.some(matcherFunc)) {
+
+      const queryExists = panelData.request?.targets.some((target) => {
+        return target.refId === options.filterData?.options;
+      });
+
+      // Only apply filter if the target query exists
+      if (queryExists) {
         panelData = {
           ...panelData,
           series: panelData.series.filter(matcherFunc),