diff --git a/src/App.tsx b/src/App.tsx
index 817c22a..1fb15a9 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -310,7 +310,11 @@ export default function App({ children }: { children: React.ReactNode }) {
                 console.log("Auto-update check already performed in this session, skipping");
                 return;
             }
-            // const isFlatpak = await invoke<boolean>('is_flatpak');
+            const isFlatpak = await invoke<boolean>('is_flatpak');
+            if (isFlatpak && (!linuxRegisteredVersion || linuxRegisteredVersion !== appVersion)) {
+                console.log("Flatpak registration not completed yet! Skipping yt-dlp auto-update...");
+                return;
+            }
             // if (isFlatpak) {
             //     console.log("Flatpak detected! Skipping yt-dlp auto-update");
             //     return;
diff --git a/src/helpers/use-linux-registerer.ts b/src/helpers/use-linux-registerer.ts
index 0544b8c..ea53ca6 100644
--- a/src/helpers/use-linux-registerer.ts
+++ b/src/helpers/use-linux-registerer.ts
@@ -4,6 +4,7 @@ import { useKvPairs } from "@/helpers/use-kvpairs";
 import { useSettingsPageStatesStore } from "@/services/store";
 import { Command } from "@tauri-apps/plugin-shell";
 import { invoke } from "@tauri-apps/api/core";
+import { useYtDlpUpdater } from "@/helpers/use-ytdlp-updater";
 
 interface FileMap {
     source: string;
@@ -14,7 +15,9 @@ interface FileMap {
 
 export function useLinuxRegisterer() {
     const { saveKvPair } = useKvPairs();
+    const { updateYtDlp } = useYtDlpUpdater();
     const appVersion = useSettingsPageStatesStore(state => state.appVersion);
+    const setYtDlpVersion = useSettingsPageStatesStore((state) => state.setYtDlpVersion);
 
     const registerToLinux = async () => {
         try {
@@ -103,6 +106,12 @@ export function useLinuxRegisterer() {
                 }
             }
             saveKvPair('linux_registered_version', appVersion);
+
+            if (isFlatpak) {
+                await updateYtDlp();
+                setYtDlpVersion(null);
+            }
+
             return { success: true, message: 'Registered successfully' }
         } catch (error) {
             console.error('Error copying files:', error);