7 Tips and Tools to Enhance Your Flatpak Experience in Linux

If you love using Flatpak applications, here are a few tips, tools, and tweaks to make your Flatpak experience better and smoother.
Warp Terminal

Slowly and steadily, Flatpak has a growing acceptance in the desktop Linux world.

It is well integrated into Fedora and many other distributions like Linux Mint, elementary, Solus, etc. prefer it over Ubuntu’s Snap.

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

1. Use Flathub to explore new Flatpak applications

This one goes without saying.

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

This is the official website from the Flatpak project, and it lists and distributes a huge number of Flatpak applications.

You can look for officially verified apps in the “Verified Apps” section, recently updated apps, new apps and popular apps.

Flathub official website home page
Flathub Website

You can have the application screenshots, description, developer information, and installation instructions on the individual application webpages.

Bonus tip: Make sure to add the Flathub repo in your system. Otherwise, you’ll see “no remote refs found similar to flathub” error while installing applications from Flathub.
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

2. Use Flatline extension to install Flatpak from the browser

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

There is also an "Install" button, but it doesn’t install the application for you. It downloads a .flatpakref file, and then you’ll have to use the command line to install from the flatpakref file.

The install button on the Fathub Apps page. It doesn’t provide a quick installation by default
Flathub Apps Page

If you have to use the command line ultimately, it doesn’t make sense to download the fltapakref file.

You can make things better by using Flatline. It’s a Mozilla Firefox extension, and it makes that Install button useful by converting it into appstream link. One more reason to use Firefox?

Flatline extension page in Mozilla Firefox's add-ons page
Flatline browser extension

This way, when you click on the "Install" button for any application on the Flathub website, it will ask you to open the link in an XDG application like the Software Center.

You can choose to install Flatpak package in software center.
Installing Flatpak from Web Browser

This also means that you should have the Flatpak support integrated into the software center.

3. Integrate Flatpak with the software center (for GNOME)

Apart from Fedora, a handful of distributions provides Flatpak support by default. You can find and install Flatpak apps from the graphical software manager.

Not all distros have that. If you are running some other distribution with the GNOME desktop environment, you can enable Flatpak support in the software center.

sudo apt install gnome-software-plugin-flatpak

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

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

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

Souk GUI software manager for Flatpak
Souk app details

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

4. Manage Flatpak permissions graphically With Flatseal

Flatseal is a graphical utility to review and modify your Flatpak applications’ permissions. This makes things a lot easier than going through the commands.

Control permissions of individual Flatpak apps
Control permissions of individual Flatpak apps

It lists all the installed Flatpak applications and shows what kind of permissions the selected application has.

You may enable or disable the permissions. Please bear in mind that disabling some permissions might impact the normal functioning of the application. You should know what you are doing.

You can install Flatseal using Flatpak, of course.

flatpak install flathub com.github.tchx84.Flatseal

5. Apply GTK system themes to Flatpak applications

You might have already noticed that most Flatpak apps don’t change their appearance as per the current system theme.

Why? Because Flatpak apps run inside a ‘container’ and don’t have access to the host filesystem, network, or physical devices.

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

Alternatively, you can make some manual effort and force the Flatpak applications to use a given theme. Here’s how to do that.

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

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

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

sudo flatpak override --env=GTK_THEME=chosen-theme 

Suggested Read 📖

Flatpak Apps Look Out of Place? Here’s How to Apply GTK Themes on Flatpak Applications
Flatpak applications don’t play along well with system themes because of their sandbox nature. With a little effort, you can make them work with system themes.

6. Update Flatpak apps and clean them

This is more for Flatpak unfriendly distributions like Ubuntu. If your distro doesn’t come baked in with Flatpak and you don’t have it integrated with the Software center, your installed Flatpak apps won’t be updated with system updates.

You can update all your installed Flatpak apps simultaneously with:

flatpak update

Not only it will update the applications, but it will also remove any unused runtimes. You don’t need to run this command manually anymore.

flatpak uninstall --unused

You can also use the GUI tool Flatsweep to clean up the residual files left after removing Flatpak applications.

Flatsweep | Flathub
Flatpak leftover cleaner

Bonus tip: While removing a Flatpak application, you can make it remove personal application data that are usually left behind in the home directory.

flatpak uninstall --delete-data package_name

7. Manage or Downgrade Flatpak Apps using Warehouse

Warehouse is an open-source app to manage Flatpak applications on your system. With this tool, you can install Flatpak from .flatpak or .flatpakref files.

More than that, you can downgrade an app if something not working properly. For that, first open Warehouse. Now, click on the three dot menu on the right side of the app, that you want to downgrade. Select Downgrade from the dropdown.

Click on the three dot menu and select downgrade option
Select Downgrade

This will fetch the releases. Once ready, select the version you needed and press the Downgrade button.

Select the version from the list to downgrade to that particular version.
Select Version

It will ask for the password. In the below screenshot, the App Amberol, a music player, has been downgraded to an older version.

Application has been downgraded and since it is no longer supported, the warning is also shown.
App Downgraded

You can enable the "Disable Updates" toggle button, so that, the version you selected will be locked and won't be upgraded to a newer version.

Downgrading an App can cause issues. You can downgrade from one version to an older. The changes will be reflected inside the warehouse app, at least for me, when reopened the app. Also, if you want to upgrade from the downgraded version (possibly to the latest), first you need to enable updates by clicking on the Enable updates button, shown in the screenshot just above.
Then, you can select the version, you needed. This time, you can press the downgrade button, but you will be upgrading the app.

What's your favorite Flatpak tip?

I deliberately didn’t add more Flatpak command tips though I was tempted to. Probably there are a few more applications and tweaks for Flatpak packages. I shared my favorite ones.

Now, it's your turn. Did you find anything new and useful? Do you use know some other tips or tools that could be added to the this list? The comment section is all yours.

About the author
Abhishek Prakash

Abhishek Prakash

Created It's FOSS 11 years ago to share my Linux adventures. Have a Master's degree in Engineering and years of IT industry experience. Huge fan of Agatha Christie detective mysteries 🕵️‍♂️

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