diff --git a/public/app/features/query/state/runRequest.test.ts b/public/app/features/query/state/runRequest.test.ts
index 6eb5095e8dc..bf789c25f62 100644
--- a/public/app/features/query/state/runRequest.test.ts
+++ b/public/app/features/query/state/runRequest.test.ts
@@ -12,6 +12,7 @@ import {
   PanelData,
 } from '@grafana/data';
 import { setEchoSrv } from '@grafana/runtime';
+import { ExpressionDatasourceRef } from '@grafana/runtime/src/utils/DataSourceWithBackend';
 import { DataQuery } from '@grafana/schema';
 
 import { deepFreeze } from '../../../../test/core/redux/reducerTester';
@@ -35,6 +36,12 @@ jest.mock('app/features/dashboard/services/DashboardSrv', () => ({
   },
 }));
 
+jest.mock('app/features/expressions/ExpressionDatasource', () => ({
+  dataSource: {
+    query: jest.fn(),
+  },
+}));
+
 class ScenarioCtx {
   ds!: DataSourceApi;
   request!: DataQueryRequest;
@@ -532,6 +539,28 @@ describe('callQueryMethod', () => {
     );
   });
 
+  it('Should not call filterQuery when targets include expression query', async () => {
+    setup({
+      targets: [
+        {
+          refId: 'A',
+          q: 'SUM(foo)',
+        },
+        {
+          refId: 'B',
+          q: 'SUM(foo2)',
+        },
+        {
+          datasource: ExpressionDatasourceRef,
+          refId: 'C',
+          q: 'SUM(foo3)',
+        },
+      ],
+      filterQuery: (query: DataQuery) => query.refId !== 'A',
+    });
+    expect(filterQuerySpy).not.toHaveBeenCalled();
+  });
+
   it('Should get ds default query when query is empty', async () => {
     setup({
       targets: [
diff --git a/public/app/features/query/state/runRequest.ts b/public/app/features/query/state/runRequest.ts
index b7f9d8589b4..7a4e6e2fdf7 100644
--- a/public/app/features/query/state/runRequest.ts
+++ b/public/app/features/query/state/runRequest.ts
@@ -201,15 +201,6 @@ export function callQueryMethod(
       : t
   );
 
-  // do not filter queries in case a custom query function is provided (for example in variable queries)
-  if (!queryFunction) {
-    request.targets = request.targets.filter((t) => datasource.filterQuery?.(t) ?? true);
-  }
-
-  if (request.targets.length === 0) {
-    return of<DataQueryResponse>({ data: [] });
-  }
-
   // If its a public datasource, just return the result. Expressions will be handled on the backend.
   if (config.publicDashboardAccessToken) {
     return from(datasource.query(request));
@@ -221,6 +212,15 @@ export function callQueryMethod(
     }
   }
 
+  // do not filter queries in case a custom query function is provided (for example in variable queries)
+  if (!queryFunction) {
+    request.targets = request.targets.filter((t) => datasource.filterQuery?.(t) ?? true);
+  }
+
+  if (request.targets.length === 0) {
+    return of<DataQueryResponse>({ data: [] });
+  }
+
   // Otherwise it is a standard datasource request
   const returnVal = queryFunction ? queryFunction(request) : datasource.query(request);
   return from(returnVal);