6 Tips and Tools to Improve Your Flatpak Experience on Linux

Slowly and steadily, Flatpak is gaining more and more acceptance in the desktop Linux world.

It is well integrated with Fedora and many other distributions like Linux Mint, Elementary, Solus, etc. prefer it to Ubuntu’s Snap.

If you love using Flatpak apps, let me share some tips, tools, and tweaks to make your Flatpak experience better and smoother.

1. Use Flathub to explore new Flatpak apps

This one goes without saying.

If you are looking for new applications in Flatpak packaging, browse the Flathub website.

This is the official website of the Flatpak project. It lists and distributes a large number of Flatpak applications.

You can find Recommended Apps in the “Editor’s Picks” section, Recently Updated Apps, New Apps, and Popular Apps.

Flathub website homepage

You can have the screenshots, description, developer information and installation instructions of the application on the web pages of each application.

bonus tip: Make sure to add the Flathub repository in your system. Otherwise, you will see the error “no remote reference found similar to flathub” when installing apps from Flathub.

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

2. Use Flatline extension to install Flatpak from browser

The Flathub website provides command line instructions to install the app.

There is also an Install button but it does not install the app for you. It downloads a .flatpakref file and then you will need to use the command line to install from the flatpakref file.

apps on flathub
Install button does not provide quick install by default

If you need to use the command line after all, it makes no sense to download the fltapakref.

You can make things better by using Flat line. It’s a Mozilla Firefox extension and it makes that install button useful by converting it to an appstream link. One more reason to use Firefox?

flat line extension
Flatline Browser Extension

This way, when you click the Install button for any app on the Flathub website, you’ll be prompted to open the link in an XDG app like the Software Center.

installing flatpak from a web browser
You can choose to install the Flatpak package in the software center

This also means that you should have Fltapak support built into the software center.

3. Integrate Flatpak with Software Center (for GNOME)

Besides Fedora, a handful of distros provide Flatpak support by default. You can find and install Flatpak applications from the graphical software manager.

Not all distributions have this. If you are running another distro with the GNOME desktop environment, you can enable Flatpak support in Software Center.

sudo apt install gnome-software-plugin-flatpak

Note that Ubuntu has moved to Snap for Software Center. The above command will also install a deb version of the GNOME Software Center. You will have two software center applications in the system.

If you enable Flatpak support in the software, you can pair it with Flatline and install Fltapak apps directly from the web browser.

Recently, there was an independent, standalone Flatpak app store called souk. However, it is no longer actively developed.

app details souk
Souk GUI software manager for Flatpak

There is also Bauh which can manage Flatpak, Snap and AppImages from a single interface.

4. Manage Flatpak permissions graphically with Flatseal

Flat seal is a graphical utility for reviewing and modifying the permissions of your Flatpak applications. This makes things much easier than going through commands.

Control individual Flatpak app permissions
Control individual Flatpak app permissions

It lists all installed Flatpak apps and shows what type of permissions the selected app has.

You can enable or disable permissions. Please keep in mind that disabling certain permissions may impact the normal operation of the app. You must know what you are doing.

You can of course install Flatseal with Flatpak.

flatpak install flathub com.github.tchx84.Flatseal

5. Apply GTK System Themes to Flatpak Applications

You may have already noticed that most Flatpak apps do not change their appearance according to the current system theme.

Why? Because Flatpak applications run in a “container” and have no access to the host filesystem, network, or physical devices.

You can choose to install themes as Flatpak to solve this problem. However, your favorite theme may not be available in Flatpak format.

Alternatively, you can do a manual effort and force Flatpak apps to use a certain theme. Here’s how.

Step 1: Give Flatpak access to the folder where theme files are kept:

sudo flatpak override --filesystem=$HOME/.themes

2nd step: List all available themes in the ~/.themes location, then provide the folder name of the selected theme to Flatpak:

sudo flatpak override --env=GTK_THEME=chosen-theme 
Comparison of Theme Switching for Flatpak Apps

If you change the system theme later, you can change the Flatpak theme the same way.

You can undo the changes using this command:

sudo flatpak override --reset

Learn more about applying the GTK theme to Flatpak apps in this article.

6. Update Flatpak apps and clean them up

It’s more for Flatpak-unfriendly distros like Ubuntu. If your distribution is not integrated with Flatpak and you have not integrated it with Software Center, your installed Flatpak applications will not be updated with system updates.

You can update all of your installed Flatpak apps simultaneously with:

flatpak update
update flatpak apps
Update Flatpak apps

Not only will it update apps, but it remove all unused runtimes. You no longer need to run this command manually.

flatpak uninstall --unused

bonus tip: When deleting a Flatpak application, you can make it delete personal application data which is usually left in the home directory.

flatpak uninstall --delete-data package_name


I deliberately did not add more tips on Flatpak orders even though I was tempted. There are probably a few more apps and tweaks for Flatpak packages. I shared my favorites.

If you know any great tips regarding Flatpak packages, share them with us in the comment section.

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Steven L. Nielsen