How to Fix Flatpak Permission Denied Errors in Linux using Flatseal

Step-by-Step Solution

Step 1: Identify the Application ID

To modify the sandbox rules of a Flatpak application, you need its reverse-DNS ID format (for instance org.gimp.GIMP or com.visualstudio.code). List installed applications:

# List all installed Flatpak applications
flatpak list --app

Step 2: Grant local filesystem access via Flatpak CLI

If an application cannot access files stored on secondary storage drives or custom directories like /mnt or /media, grant access using the override command:

# Grant access to the entire host filesystem (Filesystem=host)
flatpak override com.visualstudio.code --filesystem=host

# Or grant permission to a specific folder path (e.g. /media/external_drive)
flatpak override com.visualstudio.code --filesystem=/media/external_drive

To reset overrides back to default package permissions:

flatpak override com.visualstudio.code --reset

Step 3: Use Flatseal GUI (Recommended for Desktop users)

Flatseal is a graphical utility designed specifically for managing Flatpak permissions without terminal commands.

1. 1

   Step 1

   Install Flatseal from Flathub by running:

   BASH Copy

   flatpak install flathub com.github.tchx84.Flatseal
   

2. 2

   Step 2

   Launch Flatseal from your desktop environment's application menu (GNOME, KDE Plasma, etc.).
3. 3

   Step 3

   Select the affected application in the left sidebar.
4. 4

   Step 4

   Scroll to the Filesystem section and toggle All user files (~/) or add custom paths under Other files.

Step 4: Fix hardware acceleration and socket access errors

If an application requires GPU acceleration (Vulkan/OpenGL) or audio server access (PipeWire/PulseAudio) and crashes on launch, enable system sockets:

# Grant access to display servers (X11 / Wayland) and rendering hardware
flatpak override <APP_ID> --socket=x11 --socket=wayland --device=dri