diff --git a/x-pack/plugins/fleet/server/mocks/index.ts b/x-pack/plugins/fleet/server/mocks/index.ts
index d6620fe4c3fb9..5fab5add30fc8 100644
--- a/x-pack/plugins/fleet/server/mocks/index.ts
+++ b/x-pack/plugins/fleet/server/mocks/index.ts
@@ -62,7 +62,7 @@ export const createAppContextStartContractMock = (
     securitySetup: securityMock.createSetup(),
     securityStart: securityMock.createStart(),
     logger: loggingSystemMock.create().get(),
-    experimentalFeatures: {} as ExperimentalFeatures,
+    experimentalFeatures: { diagnosticFileUploadEnabled: true } as ExperimentalFeatures,
     isProductionMode: true,
     configInitialValue: {
       agents: { enabled: true, elasticsearch: {} },
diff --git a/x-pack/plugins/fleet/server/services/setup.test.ts b/x-pack/plugins/fleet/server/services/setup.test.ts
index 996701c920387..7d98db879910b 100644
--- a/x-pack/plugins/fleet/server/services/setup.test.ts
+++ b/x-pack/plugins/fleet/server/services/setup.test.ts
@@ -15,7 +15,9 @@ import { ensurePreconfiguredPackagesAndPolicies } from '.';
 import { appContextService } from './app_context';
 import { getInstallations } from './epm/packages';
 import { upgradeManagedPackagePolicies } from './managed_package_policies';
-import { setupFleet } from './setup';
+import { setupFleet, ensureFleetFileUploadIndices } from './setup';
+
+import { ensureFileUploadWriteIndices } from './epm/elasticsearch/template/install';
 
 jest.mock('./preconfiguration');
 jest.mock('./preconfiguration/outputs');
@@ -26,6 +28,12 @@ jest.mock('./download_source');
 jest.mock('./epm/packages');
 jest.mock('./managed_package_policies');
 jest.mock('./setup/upgrade_package_install_version');
+jest.mock('./epm/elasticsearch/template/install', () => {
+  return {
+    ...jest.requireActual('./epm/elasticsearch/template/install'),
+    ensureFileUploadWriteIndices: jest.fn(),
+  };
+});
 
 const mockedMethodThrowsError = (mockFn: jest.Mock) =>
   mockFn.mockImplementation(() => {
@@ -62,6 +70,8 @@ describe('setupFleet', () => {
 
     soClient.find.mockResolvedValue({ saved_objects: [] } as any);
     soClient.bulkGet.mockResolvedValue({ saved_objects: [] } as any);
+
+    (ensureFileUploadWriteIndices as jest.Mock).mockResolvedValue({});
   });
 
   afterEach(async () => {
@@ -128,4 +138,12 @@ describe('setupFleet', () => {
       ],
     });
   });
+
+  it('should create agent file upload write indices', async () => {
+    await ensureFleetFileUploadIndices(soClient, esClient);
+
+    expect((ensureFileUploadWriteIndices as jest.Mock).mock.calls[0][0].integrationNames).toEqual([
+      'elastic_agent',
+    ]);
+  });
 });
diff --git a/x-pack/plugins/fleet/server/services/setup.ts b/x-pack/plugins/fleet/server/services/setup.ts
index 7a35d6813cafa..da8bcfc3d093f 100644
--- a/x-pack/plugins/fleet/server/services/setup.ts
+++ b/x-pack/plugins/fleet/server/services/setup.ts
@@ -12,7 +12,11 @@ import pMap from 'p-map';
 import type { ElasticsearchClient, SavedObjectsClientContract } from '@kbn/core/server';
 import { DEFAULT_SPACE_ID } from '@kbn/spaces-plugin/common/constants';
 
-import { AUTO_UPDATE_PACKAGES, FILE_STORAGE_INTEGRATION_NAMES } from '../../common/constants';
+import {
+  AUTO_UPDATE_PACKAGES,
+  FILE_STORAGE_INTEGRATION_NAMES,
+  FLEET_ELASTIC_AGENT_PACKAGE,
+} from '../../common/constants';
 import type { PreconfigurationError } from '../../common/constants';
 import type {
   DefaultPackagesInstallationError,
@@ -199,8 +203,10 @@ export async function ensureFleetFileUploadIndices(
     pkgNames: [...FILE_STORAGE_INTEGRATION_NAMES],
   });
 
-  if (!installedFileUploadIntegrations.length) return [];
   const integrationNames = installedFileUploadIntegrations.map(({ name }) => name);
+  if (!integrationNames.includes(FLEET_ELASTIC_AGENT_PACKAGE)) {
+    integrationNames.push(FLEET_ELASTIC_AGENT_PACKAGE);
+  }
   logger.debug(`Ensuring file upload write indices for ${integrationNames}`);
   return ensureFileUploadWriteIndices({
     esClient,