diff --git a/lib/workers/repository/finalize/prune.spec.ts b/lib/workers/repository/finalize/prune.spec.ts
index 496fc82ab426f2..4048a752231d7a 100644
--- a/lib/workers/repository/finalize/prune.spec.ts
+++ b/lib/workers/repository/finalize/prune.spec.ts
@@ -82,6 +82,38 @@ describe('workers/repository/finalize/prune', () => {
       expect(platform.updatePr).toHaveBeenCalledTimes(1);
     });
 
+    it('deletes with base branches', async () => {
+      config.branchList = ['renovate/main-a'];
+      config.baseBranches = ['main', 'maint/v7'];
+      git.getBranchList.mockReturnValueOnce(
+        config.branchList.concat([
+          'renovate/main-b',
+          'renovate/maint/v7-a',
+          'renovate/maint/v7-b',
+        ]),
+      );
+      scm.isBranchModified.mockResolvedValueOnce(true);
+      scm.isBranchModified.mockResolvedValueOnce(false);
+      scm.isBranchModified.mockResolvedValueOnce(true);
+      await cleanup.pruneStaleBranches(config, config.branchList);
+      expect(git.getBranchList).toHaveBeenCalledTimes(1);
+      expect(scm.deleteBranch).toHaveBeenCalledTimes(1);
+      expect(scm.deleteBranch).toHaveBeenCalledWith('renovate/maint/v7-a');
+      expect(scm.isBranchModified).toHaveBeenCalledTimes(3);
+      expect(scm.isBranchModified).toHaveBeenCalledWith(
+        'renovate/main-b',
+        'main',
+      );
+      expect(scm.isBranchModified).toHaveBeenCalledWith(
+        'renovate/maint/v7-a',
+        'maint/v7',
+      );
+      expect(scm.isBranchModified).toHaveBeenCalledWith(
+        'renovate/maint/v7-b',
+        'maint/v7',
+      );
+    });
+
     it('does nothing on dryRun', async () => {
       config.branchList = ['renovate/a', 'renovate/b'];
       GlobalConfig.set({ dryRun: 'full' });
diff --git a/lib/workers/repository/finalize/prune.ts b/lib/workers/repository/finalize/prune.ts
index ae904b854bafc8..7d30c01f97a554 100644
--- a/lib/workers/repository/finalize/prune.ts
+++ b/lib/workers/repository/finalize/prune.ts
@@ -1,3 +1,4 @@
+import is from '@sindresorhus/is';
 import { GlobalConfig } from '../../../config/global';
 import type { RenovateConfig } from '../../../config/types';
 import { REPOSITORY_CHANGED } from '../../../constants/error-messages';
@@ -6,6 +7,8 @@ import { platform } from '../../../modules/platform';
 import { ensureComment } from '../../../modules/platform/comment';
 import { scm } from '../../../modules/platform/scm';
 import { getBranchList, setUserRepoConfig } from '../../../util/git';
+import { escapeRegExp, regEx } from '../../../util/regex';
+import { uniqueStrings } from '../../../util/string';
 import { getReconfigureBranchName } from '../reconfigure';
 
 async function cleanUpBranches(
@@ -18,16 +21,25 @@ async function cleanUpBranches(
   }
   // set Git author in case the repository is not initialized yet
   setUserRepoConfig(config);
+
+  // calculate regex to extract base branch from branch name
+  const baseBranchRe = calculateBaseBranchRegex(config);
+
   for (const branchName of remainingBranches) {
     try {
+      // get base branch from branch name if base branches are configured
+      // use default branch if no base branches are configured
+      // use defaul branch name if no match (can happen when base branches are configured later)
+      const baseBranch =
+        baseBranchRe?.exec(branchName)?.[1] ?? config.defaultBranch!;
       const pr = await platform.findPr({
         branchName,
         state: 'open',
-        targetBranch: config.baseBranch,
+        targetBranch: baseBranch,
       });
       const branchIsModified = await scm.isBranchModified(
         branchName,
-        config.defaultBranch!,
+        baseBranch,
       );
       if (pr) {
         if (branchIsModified) {
@@ -100,6 +112,32 @@ async function cleanUpBranches(
   }
 }
 
+/**
+ * Calculates a {RegExp} to extract the base branch from a branch name if base branches are configured.
+ * @param config Renovate configuration
+ */
+function calculateBaseBranchRegex(config: RenovateConfig): RegExp | null {
+  if (!config.baseBranches?.length) {
+    return null;
+  }
+
+  // calculate possible branch prefixes and escape for regex
+  const branchPrefixes = [config.branchPrefix, config.branchPrefixOld]
+    .filter(is.nonEmptyStringAndNotWhitespace)
+    .filter(uniqueStrings)
+    .map(escapeRegExp);
+
+  // calculate possible base branches and escape for regex
+  const baseBranches = config.baseBranches.map(escapeRegExp);
+
+  // create regex to extract base branche from branch name
+  const baseBranchRe = regEx(
+    `^(?:${branchPrefixes.join('|')})(${baseBranches.join('|')})-`,
+  );
+
+  return baseBranchRe;
+}
+
 export async function pruneStaleBranches(
   config: RenovateConfig,
   branchList: string[] | null | undefined,