diff --git a/sequencer.c b/sequencer.c
index f8e242b669..df89ff452d 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -1955,6 +1955,8 @@ static int do_pick_commit(struct repository *r,
 		flags |= ALLOW_EMPTY;
 	} else if (allow == 2) {
 		drop_commit = 1;
+		unlink(git_path_cherry_pick_head(r));
+		unlink(git_path_merge_msg(r));
 		fprintf(stderr,
 			_("dropping %s %s -- patch contents already upstream\n"),
 			oid_to_hex(&commit->object.oid), msg.subject);
diff --git a/t/t3424-rebase-empty.sh b/t/t3424-rebase-empty.sh
index 98fc2a558a..e1e30517ea 100755
--- a/t/t3424-rebase-empty.sh
+++ b/t/t3424-rebase-empty.sh
@@ -123,4 +123,12 @@ test_expect_success 'rebase --interactive uses default of --empty=ask' '
 	test_cmp expect actual
 '
 
+test_expect_success 'rebase --merge does not leave state laying around' '
+	git checkout -B testing localmods~2 &&
+	git rebase --merge upstream &&
+
+	test_path_is_missing .git/CHERRY_PICK_HEAD &&
+	test_path_is_missing .git/MERGE_MSG
+'
+
 test_done