diff --git a/commit-graph.c b/commit-graph.c
index ee8d5a0cdb..94d3ab4a04 100644
--- a/commit-graph.c
+++ b/commit-graph.c
@@ -2348,6 +2348,7 @@ int write_commit_graph(struct object_directory *odb,
 	init_topo_level_slab(&topo_levels);
 	ctx->topo_levels = &topo_levels;
 
+	prepare_commit_graph(ctx->r);
 	if (ctx->r->objects->commit_graph) {
 		struct commit_graph *g = ctx->r->objects->commit_graph;
 
@@ -2361,7 +2362,6 @@ int write_commit_graph(struct object_directory *odb,
 		ctx->changed_paths = 1;
 	if (!(flags & COMMIT_GRAPH_NO_WRITE_BLOOM_FILTERS)) {
 		struct commit_graph *g;
-		prepare_commit_graph_one(ctx->r, ctx->odb);
 
 		g = ctx->r->objects->commit_graph;
 
@@ -2373,10 +2373,7 @@ int write_commit_graph(struct object_directory *odb,
 	}
 
 	if (ctx->split) {
-		struct commit_graph *g;
-		prepare_commit_graph(ctx->r);
-
-		g = ctx->r->objects->commit_graph;
+		struct commit_graph *g = ctx->r->objects->commit_graph;
 
 		while (g) {
 			ctx->num_commit_graphs_before++;
@@ -2400,9 +2397,6 @@ int write_commit_graph(struct object_directory *odb,
 
 	ctx->approx_nr_objects = approximate_object_count();
 
-	if (ctx->append)
-		prepare_commit_graph_one(ctx->r, ctx->odb);
-
 	if (ctx->append && ctx->r->objects->commit_graph) {
 		struct commit_graph *g = ctx->r->objects->commit_graph;
 		for (i = 0; i < g->num_commits; i++) {
diff --git a/t/t5318-commit-graph.sh b/t/t5318-commit-graph.sh
index 2cf29f425a..5b15f1aa0f 100755
--- a/t/t5318-commit-graph.sh
+++ b/t/t5318-commit-graph.sh
@@ -446,7 +446,7 @@ test_expect_success 'warn on improper hash version' '
 	)
 '
 
-test_expect_failure 'lower layers have overflow chunk' '
+test_expect_success 'lower layers have overflow chunk' '
 	cd "$TRASH_DIRECTORY/full" &&
 	UNIX_EPOCH_ZERO="@0 +0000" &&
 	FUTURE_DATE="@2147483646 +0000" &&