diff --git a/commit-graph.c b/commit-graph.c
index f33f4fe009..3599ae664d 100644
--- a/commit-graph.c
+++ b/commit-graph.c
@@ -1687,6 +1687,12 @@ static void expire_commit_graphs(struct write_commit_graph_context *ctx)
 
 	if (ctx->split_opts && ctx->split_opts->expire_time)
 		expire_time -= ctx->split_opts->expire_time;
+	if (!ctx->split) {
+		char *chain_file_name = get_chain_filename(ctx->obj_dir);
+		unlink(chain_file_name);
+		free(chain_file_name);
+		ctx->num_commit_graphs_after = 0;
+	}
 
 	strbuf_addstr(&path, ctx->obj_dir);
 	strbuf_addstr(&path, "/info/commit-graphs");
@@ -1841,10 +1847,10 @@ int write_commit_graph(const char *obj_dir,
 
 	res = write_commit_graph_file(ctx);
 
-	if (ctx->split) {
+	if (ctx->split)
 		mark_commit_graphs(ctx);
-		expire_commit_graphs(ctx);
-	}
+
+	expire_commit_graphs(ctx);
 
 cleanup:
 	free(ctx->graph_name);
diff --git a/t/t5324-split-commit-graph.sh b/t/t5324-split-commit-graph.sh
index 3df90ae58f..e8df35c30b 100755
--- a/t/t5324-split-commit-graph.sh
+++ b/t/t5324-split-commit-graph.sh
@@ -216,6 +216,18 @@ test_expect_success 'test merge stragety constants' '
 	)
 '
 
+test_expect_success 'remove commit-graph-chain file after flattening' '
+	git clone . flatten &&
+	(
+		cd flatten &&
+		test_line_count = 2 $graphdir/commit-graph-chain &&
+		git commit-graph write --reachable &&
+		test_path_is_missing $graphdir/commit-graph-chain &&
+		ls $graphdir >graph-files &&
+		test_line_count = 0 graph-files
+	)
+'
+
 corrupt_file() {
 	file=$1
 	pos=$2