diff --git a/editor/project_converter_3_to_4.cpp b/editor/project_converter_3_to_4.cpp
index cae055c6c57..af5843d6cf5 100644
--- a/editor/project_converter_3_to_4.cpp
+++ b/editor/project_converter_3_to_4.cpp
@@ -439,6 +439,7 @@ bool ProjectConverter3To4::convert() {
 				rename_common(RenamesMap3To4::builtin_types_renames, reg_container.builtin_types_regexes, source_lines);
 				rename_input_map_scancode(source_lines, reg_container);
 				rename_common(RenamesMap3To4::input_map_renames, reg_container.input_map_regexes, source_lines);
+				custom_rename(source_lines, "config_version=4", "config_version=5");
 			} else if (file_name.ends_with(".csproj")) {
 				// TODO
 			} else if (file_name.ends_with(".import")) {
diff --git a/editor/project_manager.cpp b/editor/project_manager.cpp
index 9f9e321a9cc..52e6b478f93 100644
--- a/editor/project_manager.cpp
+++ b/editor/project_manager.cpp
@@ -2272,14 +2272,6 @@ void ProjectManager::_perform_full_project_conversion() {
 	const String &path = selected_list[0].path;
 
 	print_line("Converting project: " + path);
-
-	Ref<ConfigFile> cf;
-	cf.instantiate();
-	cf->load(path.path_join("project.godot"));
-	cf->set_value("", "config_version", GODOT4_CONFIG_VERSION);
-	cf->save(path.path_join("project.godot"));
-	_project_list->set_project_version(path, GODOT4_CONFIG_VERSION);
-
 	List<String> args;
 	args.push_back("--path");
 	args.push_back(path);
@@ -2287,6 +2279,8 @@ void ProjectManager::_perform_full_project_conversion() {
 
 	Error err = OS::get_singleton()->create_instance(args);
 	ERR_FAIL_COND(err);
+
+	_project_list->set_project_version(path, GODOT4_CONFIG_VERSION);
 }
 
 void ProjectManager::_run_project_confirm() {