How to Upgrade Flatpak on Linux Mint

Upgrading Flatpak on Linux Mint gives you access to newer application compatibility, bug fixes for sandboxing issues, and improved runtime performance. Linux Mint ships with a stable Flatpak version that works for most desktop users, but developers testing containerized applications, users troubleshooting specific app bugs, or those needing features from recent Flatpak releases may benefit from upgrading to the latest stable build.

This guide covers adding the official Flatpak PPA (Personal Package Archive) to upgrade to the latest stable version, verifying the upgrade succeeded, and managing Flatpak applications from the command line. Additionally, you will learn how to remove the PPA and downgrade to the system-provided version if compatibility issues arise. For related package management on Linux Mint, see our guide on enabling Snap on Linux Mint.

Should You Upgrade Flatpak on Linux Mint?

Linux Mint includes a stable Flatpak version tested against the distribution. Most users should stick with the system version unless they have a specific reason to upgrade:

When to upgrade:

• A Flatpak application requires a newer runtime version
• You need a specific bug fix documented in the Flatpak release notes
• You are testing containerized applications and need the latest sandboxing features
• You encounter a known issue with the system Flatpak version

Conversely, when to stay with system Flatpak:

• Your installed Flatpak applications work correctly
• You prefer stability over new features
• You want updates only after Linux Mint testing

The PPA stable channel tracks upstream Flatpak stable releases. Updates arrive faster than system packages but receive less distribution-specific testing. Application compatibility issues are rare but possible after major Flatpak version jumps.

Update Linux Mint Before Flatpak Upgrade

Before upgrading Flatpak, first update your system’s existing packages to avoid potential conflicts during the upgrade process.

Open the terminal (Ctrl+Alt+T) and run the following command:

sudo apt update && sudo apt upgrade

This command will update your package list and prompt you to upgrade any outdated packages to their latest versions.

Choose Your Flatpak PPA

Linux Mint includes Flatpak by default. To get a newer version, you can add one of the official Flatpak PPAs. The following table compares the two available options:

PPA	Channel	Stability	Best For
ppa:flatpak/stable	Upstream stable releases	Tested, reliable	Most users who want newer Flatpak features
ppa:flatpak/development	Upstream development builds	May have regressions	Developers testing specific features or debugging

Recommendation: Use the stable PPA unless you specifically need to test development features. Development builds may introduce breaking changes or application compatibility issues.

Import Stable PPA

To import the stable PPA, run:

sudo add-apt-repository ppa:flatpak/stable -y

You should see output confirming the PPA was added:

Repository: 'deb https://ppa.launchpadcontent.net/flatpak/stable/ubuntu noble main'
Description:
Latest stable versions of Flatpak.
Adding repository.
Adding deb entry to /etc/apt/sources.list.d/flatpak-ubuntu-stable-noble.sources
Adding disabled deb-src entry to /etc/apt/sources.list.d/flatpak-ubuntu-stable-noble.sources

The output shows noble for Linux Mint 22.x or jammy for Linux Mint 21.x. This reflects the underlying Ubuntu base version and is expected behavior.

Import Development PPA (Alternative)

If you need development builds instead, import the development PPA:

sudo add-apt-repository ppa:flatpak/development -y

Only use the development PPA if you are testing specific upstream features or debugging issues. Development builds receive less testing and may require manual intervention after updates.

Refresh Package List

Next, refresh the package list to include the new Flatpak packages from the PPA:

sudo apt update

The output should include a line showing packages from the Flatpak PPA:

Get:1 https://ppa.launchpadcontent.net/flatpak/stable/ubuntu noble InRelease [18.0 kB]

Upgrade Flatpak to Latest Version

Now the package manager will detect the newer Flatpak version from the PPA. Run the upgrade command:

sudo apt upgrade

The upgrade output shows the new version being installed:

The following packages will be upgraded:
  flatpak
1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Get:1 https://ppa.launchpadcontent.net/flatpak/stable/ubuntu noble/main amd64 flatpak amd64 1.16.x [1,234 kB]
Unpacking flatpak (1.16.x) over (1.14.x) ...

Confirm the upgrade completed successfully:

flatpak --version

Flatpak 1.16.1

Alternatively, if the upgrade did not apply automatically, reinstall Flatpak explicitly:

sudo apt install --reinstall flatpak

Add Flathub Repository

Flathub is the primary repository for Flatpak applications. While Linux Mint enables Flathub by default, you can verify it is configured or add it manually with the following command:

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

After running the command, verify that Flathub appears in your configured remotes:

flatpak remote-list

Name    Options
flathub system

Manage Flatpak Applications

With Flatpak upgraded, you can use the following commands to install, update, and manage applications from Flathub. Many popular applications like Steam, VS Code, and Chromium are available as Flatpaks.

Install Applications

To install an application from Flathub, specify its application ID. You can find application IDs by browsing Flathub.org and copying the ID from the app’s page. For example, to install Spotify:

flatpak install flathub com.spotify.Client

Flatpak prompts for confirmation and shows download progress:

Looking for matches…
Required runtime for com.spotify.Client/x86_64/stable (runtime/org.freedesktop.Platform/x86_64/24.08) found in remote flathub
Do you want to install it? [Y/n]: Y

Uninstall Applications

To remove an installed application, use the uninstall command with the application ID:

flatpak uninstall com.spotify.Client

Uninstalling com.spotify.Client/x86_64/stable from system

Update Applications

To update a specific application, specify its ID:

flatpak update com.spotify.Client

Looking for updates…
Nothing to do.

Alternatively, update all installed applications and runtimes at once:

flatpak update

List Installed Applications

To see all installed Flatpak applications, use the list command:

flatpak list --app

Name                  Application ID                    Version        Branch
Spotify               com.spotify.Client                1.2.31.1205    stable
VLC                   org.videolan.VLC                  3.0.20         stable

Search for Applications

Additionally, you can search Flathub for available applications. For example, searching for GIMP:

flatpak search gimp

Name                Description                                   Application ID                  Version
GIMP                Create images and edit photographs            org.gimp.GIMP                   2.10.36
GIMP (Nightly)      Development version of GIMP                   org.gimp.GIMP.Nightly           2.99.18

Manage Flatpak Remotes

The following commands help you view application details and manage your configured Flatpak repositories.

Show Application Information

To view detailed information about an installed application, use the info command:

flatpak info org.videolan.VLC

VLC - VLC media player

          ID: org.videolan.VLC
         Ref: app/org.videolan.VLC/x86_64/stable
        Arch: x86_64
      Branch: stable
     Version: 3.0.20
     License: GPL-2.0+
      Origin: flathub

List Configured Repositories

Similarly, you can view all configured Flatpak repositories:

flatpak remote-list

Add Repositories

If you need to add a third-party repository, use the remote-add command. The syntax follows this pattern:

flatpak remote-add --if-not-exists <name> <url>

Replace <name> with an identifier for the repository and <url> with the repository’s .flatpakrepo URL. For example, to add the GNOME Nightly repository:

flatpak remote-add --if-not-exists gnome-nightly https://nightly.gnome.org/gnome-nightly.flatpakrepo

Remove Repositories

Conversely, to remove a configured repository:

flatpak remote-delete <repo_name>

Replace <repo_name> with the name of the repository you want to remove.

Troubleshoot Common Flatpak Upgrade Issues

Most Flatpak upgrades complete without issues. However, application compatibility problems or PPA conflicts can occasionally occur. The following diagnostic steps help resolve common errors.

Application Fails to Launch After Upgrade

If an application fails to start after upgrading Flatpak, the runtime version may be incompatible. Check the error message:

flatpak run com.spotify.Client

error: app/com.spotify.Client/x86_64/stable requires runtime org.freedesktop.Platform/x86_64/24.08 which was not found

To resolve this, update the application and its runtime dependencies:

flatpak update com.spotify.Client

Then verify the application launches correctly after updating:

flatpak run com.spotify.Client

PPA Conflicts with System Packages

If apt upgrade shows held-back packages or dependency conflicts, you may see output like this:

The following packages have been kept back:
  flatpak libflatpak0

To diagnose the issue, check which packages are upgradable and their sources:

apt list --upgradable 2>/dev/null | grep flatpak

If conflicts persist, remove the PPA and reinstall the system Flatpak version. See the downgrade section below for complete instructions.

Downgrade to System Flatpak

When compatibility issues arise after upgrading, you can revert to the Linux Mint system version by removing the PPA and reinstalling Flatpak from the default repositories. This process preserves your installed applications while rolling back the Flatpak runtime.

Remove Flatpak PPA

First, remove the Flatpak stable PPA:

sudo add-apt-repository --remove ppa:flatpak/stable

If you added the development PPA, remove it instead:

sudo add-apt-repository --remove ppa:flatpak/development

Reinstall System Flatpak Version

After removing the PPA, refresh the package list. Then reinstall Flatpak from the default repositories:

sudo apt update

sudo apt install flatpak

APT will detect the version difference and offer to downgrade to the system package. Accept the prompt to complete the rollback.

Finally, verify the system version is now active:

flatpak --version

Flatpak 1.14.6

Remove Flatpak Completely

If you no longer need Flatpak, you can remove all applications, runtimes, and the Flatpak package itself. This process involves several steps to ensure complete cleanup.

Remove All Applications

The following command removes all Flatpak applications. Application data stored in ~/.var/app/ will remain on your system. If you want to remove application data as well (settings, caches, saved files), delete the corresponding folders in ~/.var/app/ after uninstalling.

First, uninstall all Flatpak applications:

flatpak uninstall --all

Uninstalling: com.spotify.Client/x86_64/stable
Uninstalling: org.videolan.VLC/x86_64/stable
Changes complete.

Remove Unused Runtimes

Next, clean up runtimes that are no longer required by any installed applications:

flatpak uninstall --unused

Uninstalling: org.freedesktop.Platform/x86_64/22.08
Uninstalling: org.freedesktop.Platform/x86_64/23.08
Freed 1.2 GB

Remove Flatpak Package

Finally, after removing all applications and runtimes, uninstall Flatpak and its configuration files:

sudo apt autoremove flatpak --purge

Clean Up Remaining User Data

Flatpak stores application data in your home directory. To remove all remaining Flatpak data, delete these directories:

rm -rf ~/.var/app/*
rm -rf ~/.local/share/flatpak

This permanently deletes all Flatpak application settings, caches, and locally stored data. If you plan to reinstall Flatpak later and want to preserve your application settings, skip this step.

Conclusion

You now have the latest stable Flatpak version installed from the official PPA, verified with flatpak --version, and confirmed that Flathub remains accessible via flatpak remote-list. If applications fail to launch after the upgrade, update them with flatpak update to resolve runtime mismatches. Keep the downgrade procedure available in case compatibility issues arise with specific applications. For an alternative sandboxed application format, see our guide on enabling Snap on Linux Mint.