diff --git a/app/electron/main.js b/app/electron/main.js
index ac42e8632..c52a36234 100644
--- a/app/electron/main.js
+++ b/app/electron/main.js
@@ -48,6 +48,9 @@ let resetWindowStateOnRestart = false;
 
 remote.initialize();
 
+app.setPath("userData", app.getPath("userData") + "-Electron"); // `~/.config` 下 Electron 相关文件夹名称改为 `SiYuan-Electron` https://github.com/siyuan-note/siyuan/issues/3349
+fs.rmdirSync(app.getPath("appData") + "/" + app.name, {recursive: true}); // 删除自动创建的应用目录 https://github.com/siyuan-note/siyuan/issues/13150
+
 if (!app.requestSingleInstanceLock()) {
     app.quit();
     return;
@@ -621,7 +624,6 @@ const initKernel = (workspace, port, lang) => {
 };
 
 app.setAsDefaultProtocolClient("siyuan");
-app.setPath("userData", app.getPath("userData") + "-Electron"); // `~/.config` 下 Electron 相关文件夹名称改为 `SiYuan-Electron` https://github.com/siyuan-note/siyuan/issues/3349
 
 app.commandLine.appendSwitch("disable-web-security");
 app.commandLine.appendSwitch("auto-detect", "false");