diff --git a/x-pack/plugins/entity_manager/server/lib/entities/delete_index.ts b/x-pack/plugins/entity_manager/server/lib/entities/delete_index.ts
index 433b6e392c27e..d40d9975a8820 100644
--- a/x-pack/plugins/entity_manager/server/lib/entities/delete_index.ts
+++ b/x-pack/plugins/entity_manager/server/lib/entities/delete_index.ts
@@ -7,7 +7,7 @@
 
 import { ElasticsearchClient, Logger } from '@kbn/core/server';
 import { EntityDefinition } from '@kbn/entities-schema';
-import { generateHistoryIndexName, generateLatestIndexName } from './helpers/generate_component_id';
+import { generateLatestIndexName } from './helpers/generate_component_id';
 
 export async function deleteIndices(
   esClient: ElasticsearchClient,
@@ -15,15 +15,8 @@ export async function deleteIndices(
   logger: Logger
 ) {
   try {
-    const { indices: historyIndices } = await esClient.indices.resolveIndex({
-      name: `${generateHistoryIndexName(definition)}.*`,
-      expand_wildcards: 'all',
-    });
-    const indices = [
-      ...historyIndices.map(({ name }) => name),
-      generateLatestIndexName(definition),
-    ];
-    await esClient.indices.delete({ index: indices, ignore_unavailable: true });
+    const index = generateLatestIndexName(definition);
+    await esClient.indices.delete({ index, ignore_unavailable: true });
   } catch (e) {
     logger.error(`Unable to remove entity definition index [${definition.id}}]`);
     throw e;
diff --git a/x-pack/plugins/entity_manager/server/lib/entities/uninstall_entity_definition.ts b/x-pack/plugins/entity_manager/server/lib/entities/uninstall_entity_definition.ts
index d0e0410b6e422..f8e27353082d0 100644
--- a/x-pack/plugins/entity_manager/server/lib/entities/uninstall_entity_definition.ts
+++ b/x-pack/plugins/entity_manager/server/lib/entities/uninstall_entity_definition.ts
@@ -10,63 +10,48 @@ import { SavedObjectsClientContract } from '@kbn/core-saved-objects-api-server';
 import { EntityDefinition } from '@kbn/entities-schema';
 import { Logger } from '@kbn/logging';
 import { deleteEntityDefinition } from './delete_entity_definition';
-import { deleteIndices } from './delete_index';
 import { deleteIngestPipelines } from './delete_ingest_pipeline';
-import { findEntityDefinitions } from './find_entity_definition';
 
 import { deleteTemplates } from '../manage_index_templates';
 
 import { stopTransforms } from './stop_transforms';
 
 import { deleteTransforms } from './delete_transforms';
+import { EntityClient } from '../entity_client';
 
 export async function uninstallEntityDefinition({
   definition,
   esClient,
   soClient,
   logger,
-  deleteData = false,
 }: {
   definition: EntityDefinition;
   esClient: ElasticsearchClient;
   soClient: SavedObjectsClientContract;
   logger: Logger;
-  deleteData?: boolean;
 }) {
   await stopTransforms(esClient, definition, logger);
   await deleteTransforms(esClient, definition, logger);
 
   await deleteIngestPipelines(esClient, definition, logger);
 
-  if (deleteData) {
-    await deleteIndices(esClient, definition, logger);
-  }
-
   await deleteTemplates(esClient, definition, logger);
 
   await deleteEntityDefinition(soClient, definition);
 }
 
 export async function uninstallBuiltInEntityDefinitions({
-  esClient,
-  soClient,
-  logger,
+  entityClient,
   deleteData = false,
 }: {
-  esClient: ElasticsearchClient;
-  soClient: SavedObjectsClientContract;
-  logger: Logger;
+  entityClient: EntityClient;
   deleteData?: boolean;
 }): Promise<EntityDefinition[]> {
-  const definitions = await findEntityDefinitions({
-    soClient,
-    esClient,
-    builtIn: true,
-  });
+  const { definitions } = await entityClient.getEntityDefinitions({ builtIn: true });
 
   await Promise.all(
-    definitions.map(async (definition) => {
-      await uninstallEntityDefinition({ definition, esClient, soClient, logger, deleteData });
+    definitions.map(async ({ id }) => {
+      await entityClient.deleteEntityDefinition({ id, deleteData });
     })
   );
 
diff --git a/x-pack/plugins/entity_manager/server/lib/entity_client.ts b/x-pack/plugins/entity_manager/server/lib/entity_client.ts
index 1bb1322be356f..dcb3dfab8f328 100644
--- a/x-pack/plugins/entity_manager/server/lib/entity_client.ts
+++ b/x-pack/plugins/entity_manager/server/lib/entity_client.ts
@@ -7,7 +7,7 @@
 
 import { EntityDefinition, EntityDefinitionUpdate } from '@kbn/entities-schema';
 import { SavedObjectsClientContract } from '@kbn/core-saved-objects-api-server';
-import { ElasticsearchClient } from '@kbn/core-elasticsearch-server';
+import { IScopedClusterClient } from '@kbn/core-elasticsearch-server';
 import { Logger } from '@kbn/logging';
 import {
   installEntityDefinition,
@@ -20,13 +20,14 @@ import { uninstallEntityDefinition } from './entities/uninstall_entity_definitio
 import { EntityDefinitionNotFound } from './entities/errors/entity_not_found';
 
 import { stopTransforms } from './entities/stop_transforms';
+import { deleteIndices } from './entities/delete_index';
 import { EntityDefinitionWithState } from './entities/types';
 import { EntityDefinitionUpdateConflict } from './entities/errors/entity_definition_update_conflict';
 
 export class EntityClient {
   constructor(
     private options: {
-      esClient: ElasticsearchClient;
+      clusterClient: IScopedClusterClient;
       soClient: SavedObjectsClientContract;
       logger: Logger;
     }
@@ -39,15 +40,16 @@ export class EntityClient {
     definition: EntityDefinition;
     installOnly?: boolean;
   }) {
+    const secondaryAuthClient = this.options.clusterClient.asSecondaryAuthUser;
     const installedDefinition = await installEntityDefinition({
       definition,
+      esClient: secondaryAuthClient,
       soClient: this.options.soClient,
-      esClient: this.options.esClient,
       logger: this.options.logger,
     });
 
     if (!installOnly) {
-      await startTransforms(this.options.esClient, installedDefinition, this.options.logger);
+      await startTransforms(secondaryAuthClient, installedDefinition, this.options.logger);
     }
 
     return installedDefinition;
@@ -60,10 +62,11 @@ export class EntityClient {
     id: string;
     definitionUpdate: EntityDefinitionUpdate;
   }) {
+    const secondaryAuthClient = this.options.clusterClient.asSecondaryAuthUser;
     const definition = await findEntityDefinitionById({
       id,
       soClient: this.options.soClient,
-      esClient: this.options.esClient,
+      esClient: secondaryAuthClient,
       includeState: true,
     });
 
@@ -87,22 +90,22 @@ export class EntityClient {
       definition,
       definitionUpdate,
       soClient: this.options.soClient,
-      esClient: this.options.esClient,
+      esClient: secondaryAuthClient,
       logger: this.options.logger,
     });
 
     if (shouldRestartTransforms) {
-      await startTransforms(this.options.esClient, updatedDefinition, this.options.logger);
+      await startTransforms(secondaryAuthClient, updatedDefinition, this.options.logger);
     }
     return updatedDefinition;
   }
 
   async deleteEntityDefinition({ id, deleteData = false }: { id: string; deleteData?: boolean }) {
-    const [definition] = await findEntityDefinitions({
+    const secondaryAuthClient = this.options.clusterClient.asSecondaryAuthUser;
+    const definition = await findEntityDefinitionById({
       id,
-      perPage: 1,
+      esClient: secondaryAuthClient,
       soClient: this.options.soClient,
-      esClient: this.options.esClient,
     });
 
     if (!definition) {
@@ -113,11 +116,20 @@ export class EntityClient {
 
     await uninstallEntityDefinition({
       definition,
-      deleteData,
+      esClient: secondaryAuthClient,
       soClient: this.options.soClient,
-      esClient: this.options.esClient,
       logger: this.options.logger,
     });
+
+    if (deleteData) {
+      // delete data with current user as system user does not have
+      // .entities privileges
+      await deleteIndices(
+        this.options.clusterClient.asCurrentUser,
+        definition,
+        this.options.logger
+      );
+    }
   }
 
   async getEntityDefinitions({
@@ -136,7 +148,7 @@ export class EntityClient {
     builtIn?: boolean;
   }) {
     const definitions = await findEntityDefinitions({
-      esClient: this.options.esClient,
+      esClient: this.options.clusterClient.asSecondaryAuthUser,
       soClient: this.options.soClient,
       page,
       perPage,
@@ -150,10 +162,18 @@ export class EntityClient {
   }
 
   async startEntityDefinition(definition: EntityDefinition) {
-    return startTransforms(this.options.esClient, definition, this.options.logger);
+    return startTransforms(
+      this.options.clusterClient.asSecondaryAuthUser,
+      definition,
+      this.options.logger
+    );
   }
 
   async stopEntityDefinition(definition: EntityDefinition) {
-    return stopTransforms(this.options.esClient, definition, this.options.logger);
+    return stopTransforms(
+      this.options.clusterClient.asSecondaryAuthUser,
+      definition,
+      this.options.logger
+    );
   }
 }
diff --git a/x-pack/plugins/entity_manager/server/plugin.ts b/x-pack/plugins/entity_manager/server/plugin.ts
index 2677b78042620..152b1b59b3107 100644
--- a/x-pack/plugins/entity_manager/server/plugin.ts
+++ b/x-pack/plugins/entity_manager/server/plugin.ts
@@ -99,9 +99,9 @@ export class EntityManagerServerPlugin
     request: KibanaRequest;
     coreStart: CoreStart;
   }) {
-    const esClient = coreStart.elasticsearch.client.asScoped(request).asSecondaryAuthUser;
+    const clusterClient = coreStart.elasticsearch.client.asScoped(request);
     const soClient = coreStart.savedObjects.getScopedClient(request);
-    return new EntityClient({ esClient, soClient, logger: this.logger });
+    return new EntityClient({ clusterClient, soClient, logger: this.logger });
   }
 
   public start(
diff --git a/x-pack/plugins/entity_manager/server/routes/enablement/disable.ts b/x-pack/plugins/entity_manager/server/routes/enablement/disable.ts
index 9c1c4f403636b..f8629fe46497b 100644
--- a/x-pack/plugins/entity_manager/server/routes/enablement/disable.ts
+++ b/x-pack/plugins/entity_manager/server/routes/enablement/disable.ts
@@ -49,7 +49,7 @@ export const disableEntityDiscoveryRoute = createEntityManagerServerRoute({
       deleteData: z.optional(BooleanFromString).default(false),
     }),
   }),
-  handler: async ({ context, response, params, logger, server }) => {
+  handler: async ({ context, request, response, params, logger, server, getScopedClient }) => {
     try {
       const esClientAsCurrentUser = (await context.core).elasticsearch.client.asCurrentUser;
       const canDisable = await canDisableEntityDiscovery(esClientAsCurrentUser);
@@ -62,15 +62,13 @@ export const disableEntityDiscoveryRoute = createEntityManagerServerRoute({
         });
       }
 
-      const esClient = (await context.core).elasticsearch.client.asSecondaryAuthUser;
+      const entityClient = await getScopedClient({ request });
       const soClient = (await context.core).savedObjects.getClient({
         includedHiddenTypes: [EntityDiscoveryApiKeyType.name],
       });
 
       await uninstallBuiltInEntityDefinitions({
-        soClient,
-        esClient,
-        logger,
+        entityClient,
         deleteData: params.query.deleteData,
       });
 
diff --git a/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.test.ts b/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.test.ts
index 4156ea1dbd4ea..8079e54ac9ba6 100644
--- a/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.test.ts
+++ b/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.test.ts
@@ -18,10 +18,11 @@ import type { AppClient } from '../../..';
 
 describe('EntityStoreDataClient', () => {
   const mockSavedObjectClient = savedObjectsClientMock.create();
-  const esClientMock = elasticsearchServiceMock.createScopedClusterClient().asInternalUser;
+  const clusterClientMock = elasticsearchServiceMock.createScopedClusterClient();
+  const esClientMock = clusterClientMock.asCurrentUser;
   const loggerMock = loggingSystemMock.createLogger();
   const dataClient = new EntityStoreDataClient({
-    esClient: esClientMock,
+    clusterClient: clusterClientMock,
     logger: loggerMock,
     namespace: 'default',
     soClient: mockSavedObjectClient,
diff --git a/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.ts b/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.ts
index d2e21a1d10903..5b1acaa433cd0 100644
--- a/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.ts
+++ b/x-pack/plugins/security_solution/server/lib/entity_analytics/entity_store/entity_store_data_client.ts
@@ -10,6 +10,7 @@ import type {
   ElasticsearchClient,
   SavedObjectsClientContract,
   AuditLogger,
+  IScopedClusterClient,
 } from '@kbn/core/server';
 import { EntityClient } from '@kbn/entityManager-plugin/server/lib/entity_client';
 import type { SortOrder } from '@elastic/elasticsearch/lib/api/types';
@@ -55,7 +56,7 @@ import {
 
 interface EntityStoreClientOpts {
   logger: Logger;
-  esClient: ElasticsearchClient;
+  clusterClient: IScopedClusterClient;
   namespace: string;
   soClient: SavedObjectsClientContract;
   taskManager?: TaskManagerStartContract;
@@ -79,12 +80,14 @@ export class EntityStoreDataClient {
   private assetCriticalityMigrationClient: AssetCriticalityEcsMigrationClient;
   private entityClient: EntityClient;
   private riskScoreDataClient: RiskScoreDataClient;
+  private esClient: ElasticsearchClient;
 
   constructor(private readonly options: EntityStoreClientOpts) {
-    const { esClient, logger, soClient, auditLogger, kibanaVersion, namespace } = options;
+    const { clusterClient, logger, soClient, auditLogger, kibanaVersion, namespace } = options;
+    this.esClient = clusterClient.asCurrentUser;
 
     this.entityClient = new EntityClient({
-      esClient,
+      clusterClient,
       soClient,
       logger,
     });
@@ -95,14 +98,14 @@ export class EntityStoreDataClient {
     });
 
     this.assetCriticalityMigrationClient = new AssetCriticalityEcsMigrationClient({
-      esClient,
+      esClient: this.esClient,
       logger,
       auditLogger,
     });
 
     this.riskScoreDataClient = new RiskScoreDataClient({
       soClient,
-      esClient,
+      esClient: this.esClient,
       logger,
       namespace,
       kibanaVersion,
@@ -165,7 +168,7 @@ export class EntityStoreDataClient {
     filter: string,
     pipelineDebugMode: boolean
   ) {
-    const { esClient, logger, namespace, appClient, dataViewsService } = this.options;
+    const { logger, namespace, appClient, dataViewsService } = this.options;
     const indexPatterns = await buildIndexPatterns(namespace, appClient, dataViewsService);
 
     const unitedDefinition = getUnitedEntityDefinition({
@@ -200,12 +203,12 @@ export class EntityStoreDataClient {
       // this is because the enrich policy will fail if the index does not exist with the correct fields
       await createEntityIndexComponentTemplate({
         unitedDefinition,
-        esClient,
+        esClient: this.esClient,
       });
       debugLog(`Created entity index component template`);
       await createEntityIndex({
         entityType,
-        esClient,
+        esClient: this.esClient,
         namespace,
         logger,
       });
@@ -215,12 +218,12 @@ export class EntityStoreDataClient {
       // this is because the pipeline will fail if the enrich index does not exist
       await createFieldRetentionEnrichPolicy({
         unitedDefinition,
-        esClient,
+        esClient: this.esClient,
       });
       debugLog(`Created field retention enrich policy`);
       await executeFieldRetentionEnrichPolicy({
         unitedDefinition,
-        esClient,
+        esClient: this.esClient,
         logger,
       });
       debugLog(`Executed field retention enrich policy`);
@@ -228,7 +231,7 @@ export class EntityStoreDataClient {
         debugMode: pipelineDebugMode,
         unitedDefinition,
         logger,
-        esClient,
+        esClient: this.esClient,
       });
       debugLog(`Created @platform pipeline`);
 
@@ -325,8 +328,9 @@ export class EntityStoreDataClient {
     taskManager: TaskManagerStartContract,
     options = { deleteData: false, deleteEngine: true }
   ) {
-    const { namespace, logger, esClient, appClient, dataViewsService } = this.options;
+    const { namespace, logger, appClient, dataViewsService } = this.options;
     const { deleteData, deleteEngine } = options;
+
     const descriptor = await this.engineClient.maybeGet(entityType);
     const indexPatterns = await buildIndexPatterns(namespace, appClient, dataViewsService);
     const unitedDefinition = getUnitedEntityDefinition({
@@ -348,22 +352,22 @@ export class EntityStoreDataClient {
       }
       await deleteEntityIndexComponentTemplate({
         unitedDefinition,
-        esClient,
+        esClient: this.esClient,
       });
       await deletePlatformPipeline({
         unitedDefinition,
         logger,
-        esClient,
+        esClient: this.esClient,
       });
       await deleteFieldRetentionEnrichPolicy({
         unitedDefinition,
-        esClient,
+        esClient: this.esClient,
       });
 
       if (deleteData) {
         await deleteEntityIndex({
           entityType,
-          esClient,
+          esClient: this.esClient,
           namespace,
           logger,
         });
@@ -402,7 +406,7 @@ export class EntityStoreDataClient {
     const sort = sortField ? [{ [sortField]: sortOrder }] : undefined;
     const query = filterQuery ? JSON.parse(filterQuery) : undefined;
 
-    const response = await this.options.esClient.search<Entity>({
+    const response = await this.esClient.search<Entity>({
       index,
       query,
       size: Math.min(perPage, MAX_SEARCH_RESPONSE_SIZE),
diff --git a/x-pack/plugins/security_solution/server/request_context_factory.ts b/x-pack/plugins/security_solution/server/request_context_factory.ts
index 0782fa25c71eb..d2bd579dc6b03 100644
--- a/x-pack/plugins/security_solution/server/request_context_factory.ts
+++ b/x-pack/plugins/security_solution/server/request_context_factory.ts
@@ -199,14 +199,14 @@ export class RequestContextFactory implements IRequestContextFactory {
           })
       ),
       getEntityStoreDataClient: memoize(() => {
-        const esClient = coreContext.elasticsearch.client.asCurrentUser;
+        const clusterClient = coreContext.elasticsearch.client;
         const logger = options.logger;
         const soClient = coreContext.savedObjects.client;
         return new EntityStoreDataClient({
           namespace: getSpaceId(),
+          clusterClient,
           dataViewsService,
           appClient: getAppClient(),
-          esClient,
           logger,
           soClient,
           taskManager: startPlugins.taskManager,
diff --git a/x-pack/test/api_integration/apis/entity_manager/definitions.ts b/x-pack/test/api_integration/apis/entity_manager/definitions.ts
index b51a26ad7b5ad..a1fdab08ff42a 100644
--- a/x-pack/test/api_integration/apis/entity_manager/definitions.ts
+++ b/x-pack/test/api_integration/apis/entity_manager/definitions.ts
@@ -154,7 +154,6 @@ export default function ({ getService }: FtrProviderContext) {
 
       after(async () => {
         await esDeleteAllIndices(dataForgeIndices);
-        await uninstallDefinition(supertest, { id: mockDefinition.id, deleteData: true });
         await cleanup({ client: esClient, config: dataForgeConfig, logger });
       });
 
@@ -171,6 +170,13 @@ export default function ({ getService }: FtrProviderContext) {
         const parsedSample = entityLatestSchema.safeParse(sample.hits.hits[0]._source);
         expect(parsedSample.success).to.be(true);
       });
+
+      it('should delete entities data when specified', async () => {
+        const index = generateLatestIndexName(mockDefinition);
+        expect(await esClient.indices.exists({ index })).to.be(true);
+        await uninstallDefinition(supertest, { id: mockDefinition.id, deleteData: true });
+        expect(await esClient.indices.exists({ index })).to.be(false);
+      });
     });
   });
 }