diff --git a/lib/workers/repository/finalize/index.ts b/lib/workers/repository/finalize/index.ts
index ec425dec4d6ac302e2dfa9489155d0458568510f..e530834c7ef70539e396ba413dc87d0b34cce5f9 100644
--- a/lib/workers/repository/finalize/index.ts
+++ b/lib/workers/repository/finalize/index.ts
@@ -3,7 +3,6 @@ import { logger } from '../../../logger';
 import { platform } from '../../../modules/platform';
 import * as repositoryCache from '../../../util/cache/repository';
 import { clearRenovateRefs } from '../../../util/git';
-import { configMigration } from '../config-migration';
 import { PackageFiles } from '../package-files';
 import { validateReconfigureBranch } from '../reconfigure';
 import { pruneStaleBranches } from './prune';
@@ -18,7 +17,6 @@ export async function finalizeRepo(
   branchList: string[],
 ): Promise<void> {
   await validateReconfigureBranch(config);
-  await configMigration(config, branchList);
   await repositoryCache.saveCache();
   await pruneStaleBranches(config, branchList);
   await ensureIssuesClosing();
diff --git a/lib/workers/repository/index.ts b/lib/workers/repository/index.ts
index 6a5addcc0889e263247a6a43dcb24f53bbedfb3a..2e2c1c0e4b45aca90d706b66817d34b64239856f 100644
--- a/lib/workers/repository/index.ts
+++ b/lib/workers/repository/index.ts
@@ -28,6 +28,7 @@ import {
 } from '../../util/stats';
 import { setBranchCache } from './cache';
 import { extractRepoProblems } from './common';
+import { configMigration } from './config-migration';
 import { ensureDependencyDashboard } from './dependency-dashboard';
 import handleError from './error';
 import { finalizeRepo } from './finalize';
@@ -100,6 +101,7 @@ export async function renovateRepository(
         }
         logger.debug(`Automerged but already retried once`);
       } else {
+        await configMigration(config, branchList);
         await ensureDependencyDashboard(config, branches, packageFiles);
       }
       await finalizeRepo(config, branchList);