diff --git a/midx-write.c b/midx-write.c
index 960cc46250ef8b..65e69d2de787cf 100644
--- a/midx-write.c
+++ b/midx-write.c
@@ -1474,7 +1474,8 @@ int midx_repack(struct repository *r, const char *object_dir, size_t batch_size,
 	repo_config_get_bool(r, "repack.usedeltabaseoffset", &delta_base_offset);
 	repo_config_get_bool(r, "repack.usedeltaislands", &use_delta_islands);
 
-	strvec_push(&cmd.args, "pack-objects");
+	strvec_pushl(&cmd.args, "pack-objects", "--stdin-packs", "--non-empty",
+		     NULL);
 
 	strvec_pushf(&cmd.args, "%s/pack/pack", object_dir);
 
@@ -1498,16 +1499,15 @@ int midx_repack(struct repository *r, const char *object_dir, size_t batch_size,
 	}
 
 	cmd_in = xfdopen(cmd.in, "w");
-
-	for (i = 0; i < m->num_objects; i++) {
-		struct object_id oid;
-		uint32_t pack_int_id = nth_midxed_pack_int_id(m, i);
-
-		if (!include_pack[pack_int_id])
+	for (i = 0; i < m->num_packs; i++) {
+		struct packed_git *p = m->packs[i];
+		if (!p)
 			continue;
 
-		nth_midxed_object_oid(&oid, m, i);
-		fprintf(cmd_in, "%s\n", oid_to_hex(&oid));
+		if (include_pack[i])
+			fprintf(cmd_in, "%s\n", pack_basename(p));
+		else
+			fprintf(cmd_in, "^%s\n", pack_basename(p));
 	}
 	fclose(cmd_in);