diff --git a/lib/workers/repository/index.js b/lib/workers/repository/index.js
index 7abc1b1937f25a921fab9057e63a25f76fc5eb9e..bc511240fe160ac81d6ea6cc24e4a91f03a8df14 100644
--- a/lib/workers/repository/index.js
+++ b/lib/workers/repository/index.js
@@ -85,7 +85,9 @@ async function renovateRepository(repoConfig, token, loop = 1) {
     return handleError(config, err);
   } finally {
     logger.setMeta({ repository: config.repository });
-    config.branchPrefix = commonConfig.branchPrefix;
+    config.branchPrefix = commonConfig
+      ? commonConfig.branchPrefix
+      : config.branchPrefix;
     await pruneStaleBranches(config);
     logger.info('Finished repository');
   }