Flatpak has become the standard way to install software on many Linux-powered PCs, including gaming hardware like the Steam Deck and the laptops that Endless makes available to first-time computer owners in many parts of the world.

You can easily install and remove Flatpak on many versions of Linux, but some related tasks will need extra software to get the job done. Here are the best options among them.

Removing Dippi in GNOME Software.

1.GNOME Software

GNOME Software is the app store that comes with many versions of desktop Linux. It offers excellent Flatpak integration, so it’s an easy way to discover new Flatpak apps.

You can use GNOME Software to download apps, see which ones you have currently installed, and uninstall those you’re ready to say goodbye to. When you remove an app, GNOME Software will even prompt you to remove its associated data, which would usually stay behind, taking up space.

Flatseal displaying Android Studio Flatpak information

GNOME Software can also display which sources, known as Flatpak remotes, your system is downloading apps from. you’re able to enable and disable remotes, but you can’t add new ones, so you’ll need to turn to the command line or download a third-party app for that.

If GNOME Software isn’t preinstalled on your computer, you may install it yourself. Ubuntu, for example, stopped using GNOME Software in 23.10, and versions before that came with a modified version thatdid not support Flatpaks. If you want to use Flatpaks on Ubuntu, your first step is to install GNOME Software with the Flatpak plugin:

Warehouse displaying Flatpak information for Clapper app

2.Flatseal

The ability to limit apps from accessing certain files on your PC and block off certain components, like webcams, isone of the reasons the Flatpak format exists. This is known as sandboxing, and it has been a work in progress.

Linux didn’t already have sandboxed apps like on Android and iOS, so the technology is younger, and most apps don’t ask you to grant access the way mobile apps do. Instead, they default to having a certain set of permissions, and your choice is largely to accept or reject them. For the most part, apps don’t even inform you what permissions they need.

Flatsweep cleaning Flatpak data on Fedora Silverblue.

Without sandboxing, your system can be open to all sorts of security risks. Many apps default to having access to your entire home folder, even though they may only need access to the folder storing your music or pictures.

Flatseal lets you go through the list of permissions that each of your apps has, and toggle them on or off. This offers peace of mind that a program isn’t up to something nefarious or able to gain access to your machine.

On the flip side, restricting permissions can break certain apps. Some apps don’t work as expected because they initially lack access to all your files and are limited to certain folders. You may find yourself baffled as to why a photo editor won’t open or save a file in yourDownloadsfolder, only to find that this is because the app can only see what happens in yourPicturesfolder.

Many Linux apps won’t adequately explain what’s going on, so if you don’t have an understanding of how Flatpaks and permissions work, you may conclude that the software is broken. But once you do gain understanding, the solution is usually to download andlearn how to use Flatseal.

3.Warehouse

There’s a lot of information contained within a Flatpak. Each has its own app ID and version number, runs on certain types of architecture, and may be stable or beta. If you want any of these details, you can find them within the Warehouse app. It serves as a storehouse of nearly everything you might want to know about a Flatpak.

Warehouse also mitigates one of the few minor flaws of Flatpaks: automatic updates. With Warehouse, you can tell an app to ignore updates. This way you can stick to a version that you know works, that you’re happy to stick with. This way, if a future release comes with bugs or substantial changes, it won’t impact you. Warehouse also lets you downgrade to a previous version of the app.

Like GNOME Software, Warehouse can list your available Flatpak remotes. On one hand, its list is less extensive, since it appears to ignore the repositories affiliated with your distro and, instead, shows those you may have added manually, such as Flathub. On the other hand, one huge feature it introduces is the ability to easily discover and add additional remotes. The app lists options such as the “elementaryOS AppCenter,” “GNOME Nightly,” and “KDE Testing Applications.” You can also add your own repo file or URL.

Another standout feature of Warehouse is the ability to view the folders that store your Flatpak app data. With Warehouse, it’s easy to find where an app’s data sits on your hard drive and how much space it’s taking up. Then you have the option to delete this folder.

Deleting an app’s folder can free up space on your hard drive, and can solve issues when an app is misbehaving. And Warehouse isn’t limited to the software you have currently installed. There’s a “Manage Leftover Data” option that lists and cleans up after the apps you’ve already deleted.

4.Flatsweep

Flatsweep is a simple tool that shows how much space each Flatpak app folder is taking up on your PC. Unlike Warehouse, it doesn’t attempt to do anything else.

That’s okay. Flatsweep’s singular purpose makes it a useful tool to clean the clutter that has accumulated on your PC over the years. Unlike general system cleaners, you know it won’t touch parts of your machine that could cause unexpected issues. Flatsweep is isolated just to your Flatpak apps.

Like some of the best apps designed for the GNOME desktop environment, Flatsweep does a great job performing just one task but giving you all the information you need to do it well. Open Flatsweep, wipe your files, and move on.

Flatpak Largely Just Works

Flatpak makes getting apps on Linux easier than it has ever been. But the format, or the tools built around it, still has a few kinks to work out. This is true of other alternatives, like Canonical’s Snap package format. But as time goes on, the need to install extra tools may gradually go away.