diff --git a/lib/workers/repository/cleanup.js b/lib/workers/repository/cleanup.js
index 58ee07637a545279fa264757fb2226ce186e8f78..fef678eda5b64ec3e0dbb40d91f0760048434c56 100644
--- a/lib/workers/repository/cleanup.js
+++ b/lib/workers/repository/cleanup.js
@@ -41,6 +41,11 @@ 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');