diff --git a/src-tauri/capabilities/shell.json b/src-tauri/capabilities/shell.json
index d881508..5fe39a8 100644
--- a/src-tauri/capabilities/shell.json
+++ b/src-tauri/capabilities/shell.json
@@ -66,9 +66,9 @@
           "args": true
         },
         {
-            "name": "sh",
-            "cmd": "sh",
-            "args": true
+          "name": "sh",
+          "cmd": "sh",
+          "args": true
         }
       ]
     },
@@ -131,9 +131,9 @@
           "args": true
         },
         {
-            "name": "sh",
-            "cmd": "sh",
-            "args": true
+          "name": "sh",
+          "cmd": "sh",
+          "args": true
         }
       ]
     }
diff --git a/src-tauri/tauri.linux-flatpak.conf.json b/src-tauri/tauri.linux-flatpak.conf.json
index f6e82cb..4cceabb 100644
--- a/src-tauri/tauri.linux-flatpak.conf.json
+++ b/src-tauri/tauri.linux-flatpak.conf.json
@@ -37,7 +37,6 @@
             "icons/icon.ico"
         ],
         "externalBin": [
-            "binaries/yt-dlp",
             "binaries/deno"
         ],
         "resources": {
diff --git a/src/App.tsx b/src/App.tsx
index d46e48a..62b16b0 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -257,7 +257,10 @@ export default function App({ children }: { children: React.ReactNode }) {
         const fetchYtDlpVersion = async () => {
             setIsFetchingYtDlpVersion(true);
             try {
-                const command = Command.sidecar('binaries/yt-dlp', ['--version']);
+                const isFlatpak = await invoke<boolean>('is_flatpak');
+                const command = isFlatpak
+                ? Command.create('sh', ['-c', `yt-dlp --version`])
+                : Command.sidecar('binaries/yt-dlp', ['--version']);
                 const output = await command.execute();
                 if (output.code === 0) {
                     const version = output.stdout.trim();
diff --git a/src/helpers/use-downloader.ts b/src/helpers/use-downloader.ts
index 96fcd7f..1fb44b5 100644
--- a/src/helpers/use-downloader.ts
+++ b/src/helpers/use-downloader.ts
@@ -196,7 +196,10 @@ export default function useDownloader() {
                 }
             }
 
-            const command = Command.sidecar('binaries/yt-dlp', args);
+            const isFlatpak = await invoke<boolean>('is_flatpak');
+            const command = isFlatpak
+            ? Command.create('sh', ['-c', `yt-dlp ${args.map(arg => arg.includes(' ') ? `"${arg}"` : arg).join(' ')}`])
+            : Command.sidecar('binaries/yt-dlp', args);
 
             let jsonOutput = '';
 
@@ -557,7 +560,10 @@ export default function useDownloader() {
         }
 
         console.log('Starting download with args:', args);
-        const command = Command.sidecar('binaries/yt-dlp', args);
+        const isFlatpak = await invoke<boolean>('is_flatpak');
+        const command = isFlatpak
+        ? Command.create('sh', ['-c', `yt-dlp ${args.map(arg => arg.includes(' ') ? `"${arg}"` : arg).join(' ')}`])
+        : Command.sidecar('binaries/yt-dlp', args);
 
         command.on('close', async (data) => {
             if (data.code !== 0) {
diff --git a/src/helpers/use-ytdlp-updater.ts b/src/helpers/use-ytdlp-updater.ts
index fc6cec1..50d562b 100644
--- a/src/helpers/use-ytdlp-updater.ts
+++ b/src/helpers/use-ytdlp-updater.ts
@@ -21,7 +21,13 @@ export function useYtDlpUpdater() {
         setIsUpdatingYtDlp(true);
         LOG.info('NEODLP', 'Updating yt-dlp to latest version');
         try {
-            const command = currentPlatform === 'linux' && !isFlatpak ? Command.create('pkexec', ['yt-dlp', '--update-to', ytDlpUpdateChannel]) : Command.sidecar('binaries/yt-dlp', ['--update-to', ytDlpUpdateChannel]);
+            const command = currentPlatform === 'linux' && isFlatpak
+            ? ytDlpUpdateChannel === 'nightly'
+              ? Command.create('sh', ['-c', 'pip3 install -U --pre "yt-dlp[default,curl-cffi]"'])
+              : Command.create('sh', ['-c', 'pip3 install -U "yt-dlp[default,curl-cffi]"'])
+            : currentPlatform === 'linux'
+              ? Command.create('pkexec', ['yt-dlp', '--update-to', ytDlpUpdateChannel])
+              : Command.sidecar('binaries/yt-dlp', ['--update-to', ytDlpUpdateChannel]);
             const output = await command.execute();
             if (output.code === 0) {
                 console.log("yt-dlp updated successfully:", output.stdout);