diff --git a/src/main.ts b/src/main.ts
index 3256290..eef1b58 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -86,7 +86,7 @@ const DEFAULT_SETTINGS: RemotelySavePluginSettings = {
   deleteToWhere: "system",
   agreeToUseSyncV3: false,
   conflictAction: "keep_newer",
-  howToCleanEmptyFolder: "skip",
+  howToCleanEmptyFolder: "clean_both",
   protectModifyPercentage: 50,
   syncDirection: "bidirectional",
   obfuscateSettingFile: true,
@@ -896,7 +896,7 @@ export default class RemotelySavePlugin extends Plugin {
       this.settings.conflictAction = "keep_newer";
     }
     if (this.settings.howToCleanEmptyFolder === undefined) {
-      this.settings.howToCleanEmptyFolder = "skip";
+      this.settings.howToCleanEmptyFolder = "clean_both";
     }
     if (this.settings.protectModifyPercentage === undefined) {
       this.settings.protectModifyPercentage = 50;
diff --git a/src/settings.ts b/src/settings.ts
index 8ec65db..f376ffe 100644
--- a/src/settings.ts
+++ b/src/settings.ts
@@ -2018,7 +2018,7 @@ export class RemotelySaveSettingTab extends PluginSettingTab {
           t("settings_cleanemptyfolder_clean_both")
         );
         dropdown
-          .setValue(this.plugin.settings.howToCleanEmptyFolder ?? "skip")
+          .setValue(this.plugin.settings.howToCleanEmptyFolder ?? "clean_both")
           .onChange(async (val) => {
             this.plugin.settings.howToCleanEmptyFolder =
               val as EmptyFolderCleanType;
diff --git a/src/sync.ts b/src/sync.ts
index 69bed26..36e31a8 100644
--- a/src/sync.ts
+++ b/src/sync.ts
@@ -1364,7 +1364,7 @@ export async function syncer(
     step = 6;
     mixedEntityMappings = await getSyncPlanInplace(
       mixedEntityMappings,
-      settings.howToCleanEmptyFolder ?? "skip",
+      settings.howToCleanEmptyFolder ?? "clean_both",
       settings.skipSizeLargerThan ?? -1,
       settings.conflictAction ?? "keep_newer",
       settings.syncDirection ?? "bidirectional",