diff --git a/ls-refs.c b/ls-refs.c
index 88f6c3f60d..e6a2dbd962 100644
--- a/ls-refs.c
+++ b/ls-refs.c
@@ -105,7 +105,7 @@ static int send_ref(const char *refname, const struct object_id *oid,
 	}
 
 	strbuf_addch(&refline, '\n');
-	packet_write(1, refline.buf, refline.len);
+	packet_fwrite(stdout, refline.buf, refline.len);
 
 	strbuf_release(&refline);
 	return 0;
@@ -171,7 +171,7 @@ int ls_refs(struct repository *r, struct strvec *keys,
 		strvec_push(&data.prefixes, "");
 	for_each_fullref_in_prefixes(get_git_namespace(), data.prefixes.v,
 				     send_ref, &data, 0);
-	packet_flush(1);
+	packet_fflush(stdout);
 	strvec_clear(&data.prefixes);
 	return 0;
 }
diff --git a/upload-pack.c b/upload-pack.c
index 297b76fcb4..0ed377b1fb 100644
--- a/upload-pack.c
+++ b/upload-pack.c
@@ -1207,7 +1207,7 @@ static int send_ref(const char *refname, const struct object_id *oid,
 
 		format_symref_info(&symref_info, &data->symref);
 		format_session_id(&session_id, data);
-		packet_write_fmt(1, "%s %s%c%s%s%s%s%s%s%s object-format=%s agent=%s\n",
+		packet_fwrite_fmt(stdout, "%s %s%c%s%s%s%s%s%s%s object-format=%s agent=%s\n",
 			     oid_to_hex(oid), refname_nons,
 			     0, capabilities,
 			     (data->allow_uor & ALLOW_TIP_SHA1) ?
@@ -1223,11 +1223,11 @@ static int send_ref(const char *refname, const struct object_id *oid,
 		strbuf_release(&symref_info);
 		strbuf_release(&session_id);
 	} else {
-		packet_write_fmt(1, "%s %s\n", oid_to_hex(oid), refname_nons);
+		packet_fwrite_fmt(stdout, "%s %s\n", oid_to_hex(oid), refname_nons);
 	}
 	capabilities = NULL;
 	if (!peel_iterated_oid(oid, &peeled))
-		packet_write_fmt(1, "%s %s^{}\n", oid_to_hex(&peeled), refname_nons);
+		packet_fwrite_fmt(stdout, "%s %s^{}\n", oid_to_hex(&peeled), refname_nons);
 	return 0;
 }
 
@@ -1348,6 +1348,11 @@ void upload_pack(struct upload_pack_options *options)
 		reset_timeout(data.timeout);
 		head_ref_namespaced(send_ref, &data);
 		for_each_namespaced_ref(send_ref, &data);
+		/*
+		 * fflush stdout before calling advertise_shallow_grafts because send_ref
+		 * uses stdio.
+		 */
+		fflush_or_die(stdout);
 		advertise_shallow_grafts(1);
 		packet_flush(1);
 	} else {