diff --git a/package.json b/package.json
index b9c06ec..aa0a601 100644
--- a/package.json
+++ b/package.json
@@ -2,7 +2,7 @@
   "name": "ovm",
   "description": "Obsidian Vaults Manager",
   "type": "commonjs",
-  "version": "0.6.3",
+  "version": "0.6.4",
   "license": "GPL-3.0-only",
   "author": "Masoud Ghorbani",
   "homepage": "https://github.com/msudgh/ovm",
diff --git a/src/providers/plugins.ts b/src/providers/plugins.ts
index 37a676a..d3cffa4 100644
--- a/src/providers/plugins.ts
+++ b/src/providers/plugins.ts
@@ -19,7 +19,6 @@ export const removePluginDir = async (pluginId: string, vaultPath: string) => {
   childLogger.debug(`Remove plugin`)
 
   await rm(pluginDir, { recursive: true, force: true })
-  await modifyCommunityPlugins({ id: pluginId }, vaultPath, 'disable')
 
   childLogger.debug(`Removed plugin`)
 }
@@ -30,11 +29,15 @@ export const listInstalledPlugins = async (vaultPath: string) => {
 
   await access(pluginsPath, constants.R_OK)
 
-  const existingDirs = await readdir(pluginsPath)
+  const entries = await readdir(pluginsPath, {
+    withFileTypes: true,
+  })
 
-  installedPlugins = existingDirs.map((plugin) => ({
-    id: plugin,
-  }))
+  installedPlugins = entries
+    .filter(({ isDirectory }) => isDirectory())
+    .map((dir) => ({
+      id: dir.name,
+    }))
 
   return installedPlugins
 }
diff --git a/src/services/prune.ts b/src/services/prune.ts
index 9dd7025..d254269 100644
--- a/src/services/prune.ts
+++ b/src/services/prune.ts
@@ -1,6 +1,10 @@
 import { ArgInput } from '@oclif/core/lib/parser'
 import { each } from 'async'
-import { listInstalledPlugins, removePluginDir } from '../providers/plugins'
+import {
+  listInstalledPlugins,
+  modifyCommunityPlugins,
+  removePluginDir,
+} from '../providers/plugins'
 import { getSelectedVaults, mapVaultsIteratorItem } from '../providers/vaults'
 import {
   FactoryFlagsWithVaults,
@@ -28,6 +32,7 @@ const pruneVaultIterator: PruneCommandIterator = async (item) => {
 
   for (const plugin of toBePruned) {
     await removePluginDir(plugin.id, vault.path)
+    await modifyCommunityPlugins({ id: plugin.id }, vault.path, 'disable')
   }
 
   childLogger.info(`Pruned ${toBePruned.length} plugins`, {