diff --git a/lib/workers/repository/cleanup.js b/lib/workers/repository/cleanup.js
index fef678eda5b64ec3e0dbb40d91f0760048434c56..58ee07637a545279fa264757fb2226ce186e8f78 100644
--- a/lib/workers/repository/cleanup.js
+++ b/lib/workers/repository/cleanup.js
@@ -41,11 +41,6 @@ async function pruneStaleBranches(config) {
     logger.debug('No branches to clean up');
     return;
   }
-  // istanbul ignore if
-  if (config.baseBranches && config.baseBranches.length) {
-    logger.info('Skipping cleanup for multiple baseBranches');
-    return;
-  }
   for (const branchName of remainingBranches) {
     logger.info({ branch: branchName }, `Deleting orphan branch`);
     const pr = await platform.findPr(branchName, null, 'open');