diff --git a/lib/workers/repository/cleanup.js b/lib/workers/repository/cleanup.js
index f1c921b24b604731f84bba5275409d00ca5814c5..e96707a95952d1d6ec31d1c117a8bffc09c88198 100644
--- a/lib/workers/repository/cleanup.js
+++ b/lib/workers/repository/cleanup.js
@@ -12,10 +12,12 @@ async function pruneStaleBranches(config) {
     logger.debug('No branchList');
     return;
   }
+  logger.debug({ branchList }, 'branchList');
   let renovateBranches = await platform.getAllRenovateBranches(
     config.branchPrefix
   );
   if (!(renovateBranches && renovateBranches.length)) {
+    logger.debug('No renovate branches found');
     return;
   }
   logger.debug({ branchList, renovateBranches });
diff --git a/lib/workers/repository/index.js b/lib/workers/repository/index.js
index b451acf8f1fbd37501047e3f5ae69410d088f107..7abc1b1937f25a921fab9057e63a25f76fc5eb9e 100644
--- a/lib/workers/repository/index.js
+++ b/lib/workers/repository/index.js
@@ -18,6 +18,7 @@ async function renovateRepository(repoConfig, token, loop = 1) {
   logger.setMeta({ repository: config.repository });
   logger.info('Renovating repository');
   logger.trace({ config, loop }, 'renovateRepository()');
+  let commonConfig;
   try {
     if (loop > 5) {
       throw new Error('loops>5');
@@ -28,7 +29,7 @@ async function renovateRepository(repoConfig, token, loop = 1) {
     if (config.baseBranches && config.baseBranches.length) {
       // At this point we know if we have multiple branches
       // Do the following for every branch
-      const commonConfig = JSON.parse(JSON.stringify(config));
+      commonConfig = JSON.parse(JSON.stringify(config));
       const configs = [];
       logger.info({ baseBranches: config.baseBranches }, 'baseBranches');
       for (const [index, baseBranch] of commonConfig.baseBranches.entries()) {
@@ -84,6 +85,7 @@ async function renovateRepository(repoConfig, token, loop = 1) {
     return handleError(config, err);
   } finally {
     logger.setMeta({ repository: config.repository });
+    config.branchPrefix = commonConfig.branchPrefix;
     await pruneStaleBranches(config);
     logger.info('Finished repository');
   }