How to Install A Flatpak (.flatpakref) Package in Ubuntu Linux [Beginner’s Guide]

This is a beginner’s guide shows how to install a Flatpak app package via local .flatpakref, an URL link, or a software repository.

Some popular Linux has added Flatpak support out-of-the-box. User can even install Flatpak via system’s default package manager, including Fedora‘s Gnome Software, Linux Mint‘s software manager, and Manjaro‘s Pamac.

However, many other Linux does not support this package format, including the popular Ubuntu and Debian. So, I’m here to write this tutorial and hope it could help.

Why Flatpak

As you may know, Linux has the most popular libraries installed as separated packages. Native app packages can be quite small in file size, because they share these dependency libraries that are already in system.

As a result, a small app can do a great job! However, free open-source world is moving so fast that core system libraries are always outdated. New apps (or versions) need updated libraries, but Linux system has an old version required by other core components. So, it causes problems.

To workaround this issue, Flatpak, Snap, and AppImage packages born! They include the application packages with most run-time libraries bundled, make possible to run apps with new features even on old systems.

The downside is that they require more disk spaces due to bundled run-time libraries. And, they run in sandbox with problem communicating with other system apps. Though, developer are now working on the issue.

As more and more software developers publish Linux package via Flatpak and AppImage, though Ubuntu sticks to Snap. It’s hard to avoid these package formats today in Linux.

Install A Flatpak Package

Usually, we can get a Flatpak package via 3 different ways: download from software website, using direct URL link, or from a software repository (e.g., Flathub).

First of all, search for and open ‘terminal’ from system start menu or ‘Activities’ overview, and continue the steps below

Enable Flatpak support

Ubuntu & Debian does not support this package format out-of-the-box. But, user can simply run the command below to enable it:

sudo apt install flatpak

The old Ubuntu 16.04 and Ubuntu 18.04 can even enable Flatpak support via this PPA.

For other Linux, follow the official setup guide.

Install local .flatpakref (or .flatpak) file

In case you already downloaded a software package with .flatpakref or .flatpak file extension. Install it, by running command:

flatpak install /PATH/TO/filename.flatpakref

Users mostly save files in ‘Downloads’ folder, so the command can be: flatpak install ~/Downloads/filename.flatpakref .

Tip: Drag and drop file into terminal can insert /PATH/TO/FILE automatically.
merilyn@Jammy:~$ flatpak install ~/Downloads/org.gnome.Boxes.flatpakref

org.gnome.Boxes permissions:
    ipc                network                  fallback-x11   pulseaudio
    wayland            x11                      devices        file access [1]
    dbus access [2]    system dbus access [3]

    [1] /var/lib/AccountsService/icons:ro, host, xdg-run/dconf,
    [2] ca.desrt.dconf, org.freedesktop.secrets, org.gnome.ControlCenter
    [3] org.freedesktop.Accounts, org.freedesktop.timedate1

        ID                                 Branch Op Remote  Download
 1.     org.gnome.Boxes.Extension.OsinfoDb stable i  flathub < 690.6 kB
 2.     org.gnome.Boxes.Locale             stable i  flathub   < 6.2 MB (partial)
 3.     org.gnome.Boxes                    stable i  flathub  < 52.4 MB

Proceed with these changes to the system installation? [Y/n]: 

The command will output the permissions the app package required, information about the packages and run-times to install. User has to either type "y" to continue or type "n" to stop it.

Install via an URL

Without downloading the .flatpakref file, user may select to copy the download URL into clipboard, and use the command below to install it:

flatpak install url-link-to-flatpakref

I like this method, as it leaves my 'Downloads' folder clean.

Install Flatpak from software repository

By adding a software repository, usually, user can simply run the command below to install a package:


For example, use flatpak install flathub org.gnome.Boxes to install Gnome Boxes.

Most Linux can use the single command below to add Flathub repository:

flatpak remote-add --if-not-exists flathub

How to List Installed & Remove Flatpak package

To tell all installed Flatpak applications in your system, use command:

flatpak list --app

You may skip the --app flag, so it outputs all packages including the run-time libraries installed as dependency:

flatpak list

To list runtime separately, use command

flatpak list --runtime

And, to remove a flatpak package, use command:

flatpak uninstall --delete-data app-ID

For example, use flatpak uninstall --delete-data io.github.seadve.Kooha to remove Kooha. If you want to keep the personal data files, skip --delete-data section.

Manage Flatpak App Permissions

Default permissions are mostly good. But if you want, it's possible to manager the accessibility of network, file-system, and hardware devices, such as printer, bluetooth, speaker and camera.

That's quite a lot of command options, you may go to the official documentation for details.

For desktop PC/laptop, I'd always recommend Flatseal, a graphical tool to manage Flatpak apps:

User can install the app either by visiting the link above, or run the command below in a terminal window:

flatpak install

That's all. Enjoy!

Hi, I'm Merilyn Ne, a computer geek working on Ubuntu Linux for many years and would like to write useful tips for beginners. Forgive me for language mistakes. I'm not a native speaker of English.