Flatpak Template Installation (Updated November 2025)

Original forum link: https://forum.qubes-os.org/t/37301
Original poster: idk
Created at: 2025-11-11 02:30:31
Posts count: 13
Likes count: 12

Flatpak Template Installation (Updated November 2025)

Target: Debian 12/13 - XFCE template

Disclaimer: This guide resolves the problems I encountered installing Flatpak support in my templates while reasonably adhering to current Qubes OS security guidelines. The guide covers installing Flatpak containers in the system workspace (templateVM) and in user space (AppVM, StandaloneVM). This guide aims to be as simple and user-friendly as possible.

Thanks to KitsuneNoBaka and solene for their help.

Note: It is assumed that the user is already familiar with Qubes OS and its security approach (necessary restrictions) when manipulating system components!

Steps to follow:

For Debian XFCE Template

(Assumes Qubes OS configuration - anonymous updates - proxy - sys-Whonix enabled)

Start the template.
Open the Synaptic Package Manager.
Install the Gnome Store and Flatpak support packages:

gnome-software gnome-software-common gnome-software-plugin-flatpak libflatpak0
End of installation

# Flatpak configuration in the system template (immutable) #

Open a system terminal
Enter the following commands:

export all_proxy=http://127.0.0.1:8082/

#This opens a communication channel through the sys-Whonix proxy connection

flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

#This adds a temporary Flatpak repository address (config.system)

Enable communication from the proxy for updating the application catalog in the Gnome Store with the command:

export http_proxy=http://127.0.0.1:8082/

Launch the GNOME Software Store from the same terminal with the command:

gnome-software

Install your chosen Flatpak apps
Enjoy :)

The template should now be able to install any Flatpak app and be deployed without changes persisting outside the template.

Flatpak configuration in a user space (deployment for persistence in AppVM Qubes)

Repeat the GNOME Store and Flatpak installation steps using the Synaptic package manager.
Close the template.

The rest of the configuration and app installation must be done from an AppVM or StandaloneVM created from the template.

Create an AppVM or StandaloneVM from the flatpak-user template created.
Open a system terminal.
Enter the command:

flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

This adds the Flatpak repository address (user space configuration)

Open the GNOME Store from the same terminal with the command:

gnome-software

The store should now display the applications from the Debian repository and include the Flathub catalog. The goal is to ensure that in the installation source selector in the upper right corner, alongside the traditional (deb) option, the option for (flatpak) should appear, but with the label "user." This means that the app will be installed in the user space of the AppVM and will remain even after the qube is restarted.

Install apps.
Enjoy :)

Manual update of the Flatpak container and runtime

Updating Flatpak installed in system space must be done from the template in this installation mode.

Note: It is recommended to disable the automatic updates option in the GNOME Store for template mode, as changes will not persist in Qubes created from them and will only be a waste of internet bandwidth.

For user space installations, this must be done from each Qube separately where apps were installed.

To update manually in all cases, run the command in a terminal:

flatpak upgrade -y

End of guide.

Regards,