diff --git a/dvc/repo/experiments/executor/local.py b/dvc/repo/experiments/executor/local.py
index d45a4ed22..f9ff8dce0 100644
--- a/dvc/repo/experiments/executor/local.py
+++ b/dvc/repo/experiments/executor/local.py
@@ -90,6 +90,11 @@ class TempDirExecutor(BaseLocalExecutor):
         head = EXEC_BRANCH if branch else EXEC_HEAD
         self.scm.checkout(head, detach=True)
         merge_rev = self.scm.get_ref(EXEC_MERGE)
+
+        for ref in (EXEC_HEAD, EXEC_MERGE, EXEC_BASELINE):
+            if scm.get_ref(ref):
+                scm.remove_ref(ref)
+
         try:
             self.scm.merge(merge_rev, squash=True, commit=False)
         except _SCMError as exc:
diff --git a/tests/unit/repo/experiments/queue/test_local.py b/tests/unit/repo/experiments/queue/test_local.py
index e24d3a92a..8d38af002 100644
--- a/tests/unit/repo/experiments/queue/test_local.py
+++ b/tests/unit/repo/experiments/queue/test_local.py
@@ -5,6 +5,8 @@ from celery import shared_task
 from flaky.flaky_decorator import flaky
 
 from dvc.repo.experiments.exceptions import UnresolvedExpNamesError
+from dvc.repo.experiments.executor.local import TempDirExecutor
+from dvc.repo.experiments.refs import EXEC_BASELINE, EXEC_HEAD, EXEC_MERGE
 
 
 def test_shutdown_no_tasks(test_queue, mocker):
@@ -104,3 +106,17 @@ def test_celery_queue_kill(test_queue, mocker):
     spy = mocker.patch.object(test_queue.proc, "kill")
     test_queue.kill("bar")
     assert spy.called_once_with(mock_entry.stash_rev)
+
+
+def test_queue_clean_workspace_refs(git_dir, tmp_dir):
+
+    rev = git_dir.scm.get_rev()
+    exec_heads = (EXEC_MERGE, EXEC_BASELINE, EXEC_HEAD)
+    for ref in exec_heads:
+        git_dir.scm.set_ref(ref, rev)
+
+    temp_dir_executor = TempDirExecutor(str(tmp_dir), str(tmp_dir), rev)
+    temp_dir_executor.init_git(git_dir.scm)
+
+    for ref in exec_heads:
+        assert git_dir.scm.get_ref(ref) is None