How to Install and Use Flatpak Apps on Raspberry Pi OS

I generally use APT to install apps on Raspberry Pi OS, but it isn’t always an option. That’s when you might want to consider Flatpak. In this guide, I’ll show you how to set it up and easily install awesome desktop apps.

Flatpak is a universal package manager for Linux that installs desktop applications as standalone containers. The Flatpak utility can be installed on Raspberry Pi OS using APT. After installation, Flatpak apps can be installed from repositories like Flathub.

Flatpak is a contender for one of the best package managers to get desktop apps working on any Linux distribution. I’ll briefly discuss when it beats other alternatives, and then I’ll walk you through installing Flatpak apps on your system.

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Flatpak – A Universal Package Manager for Linux

Raspberry Pi OS is based on Debian, so it uses APT as its package manager. APT is a great way to get the programs I want—most of the time.

I’ve run into situations, however, when APT is not ideal. For example, some programs are:

• Unavailable in the default repository.
• Complex to install, using a nonstandard process that makes it difficult to maintain.
• Not supported on Raspberry Pi OS or on Linux as a whole.

That’s when I turn to Flatpak: it’s an easier and safer way to install desktop applications.

Before I show you how to install Flatpak, let’s discuss why you would want to use it in the first place, and how it’s different from other package managers.

When to Use Flatpak

There are a few scenarios where I prefer using Flatpak to install programs.

Simplifying Installation – If I want a particular desktop application but find out that it takes too many workarounds to install, I’ll install the Flatpak version instead. That’s because Flatpak uses containerization to bundle everything the program needs into a standalone package.

Some examples of this include ONLYOFFICE, which often requires troubleshooting during installation, depending on your system configuration. With Flatpak, it’s a single command to get it installed.

Overcoming Dependency Conflicts – Sometimes, I can’t install a specific program because it’s blocked by a dependency version that’s either a) too new, or b) conflicts with other packages on my system. Flatpak solves this problem by keeping dependencies separate per package.

For example, this type of blockage occurs when trying to install Minecraft: Java Edition on Raspberry Pi OS. Minecraft requires a newer Java version than what’s available in the default repository. But if you install it with Flatpak, these dependency conflicts are resolved.

Installing Programs Not Available on Raspberry Pi OS – Now and then, I’ll need an application that isn’t supported on Raspberry Pi OS. Or, it may have a GitHub with poor instructions on how to build from source. In the past, I might have given up, but with Flatpak, I can often install it with ease.

One example includes Beekeeper Studio, a graphical database manager. It might not be officially supported on Raspberry Pi OS, but with Flatpak, I was still able to install it—neat!

What’s the Difference Between Flatpak and Other Package Managers?

Why does Flatpak exist when we already have APT, Snap, and Docker?
Flatpak has some upsides (and downsides) over these other package managers.

Flatpak vs. APT

APT is the default package manager on Raspberry Pi OS. Flatpak differs from APT because it installs applications as standalones that don’t depend on other packages on the system.

Flatpak vs. Docker

Next, there’s Docker, a container manager. As much as I love Docker, it’s more difficult to learn and is better suited for servers. Flatpak, on the other hand, is user-friendly and excels for programs that you use directly in your GUI—copy/pasting, dragging files, etc.

Flatpak vs. Snap

Finally, we have Snap, an alternate package manager first created for Ubuntu. Snap and Flatpak are the most similar in their goals and design. However, Flatpak is open source, more universal across distros, and has better performance for desktop programs.

I make Flatpak sound pretty amazing here, but it’s far from perfect. At the end of the article, I’ll cover more of its limitations.

How to Install Flatpak on Raspberry Pi

Seeing is believing, and since Flatpak is free, it costs you nothing to take it for a test drive.

Let’s start by installing the Flatpak utility itself:

• Install Flatpak using APT:
  sudo apt install flatpak
• Add the main repository:
  sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
• Restart your system:
  sudo reboot

After that, you can check if Flatpak is installed properly by simply running the command:
flatpak

Quick note: If you find it hard to remember all these commands, I’ve put them all on a one-page cheat sheet. You can download it for free here so you have it handy whenever you're working on a project.

Where to Find Flatpak Apps?

Now that you’ve got Flatpak, let’s learn where you can find free apps to install.

Flathub: The Linux App Store

Flatpak can be installed from any source that you’ve added. Earlier during installation, we added the most well-known Flatpak repository: Flathub. Flathub is like the Google Play Store, but it specifically finds Flatpak apps for Linux.

Note: Not all programs you see on Flathub can be installed on Raspberry Pi OS. When searching, make sure to mark the “aarch64” filter. This will let you find programs that work with the Raspberry Pi’s CPU.

Most users will probably get their Flatpak apps from Flathub. There are productivity programs like this PDF editor, games like Runescape, education, audio/video like Audacity, and even proprietary apps like Deezer.

I want to stress that, besides the popular desktop apps, Flathub has tons of programs that might have been unusual to find on Raspberry Pi OS in the past. And in my opinion, that’s one of the best things about Flatpak.

Other Flatpak Sources

Can you install Flatpak apps from repositories other than Flathub?
Sure, you can add sources such as:

• ElementaryOS Flatpaks – (https://flatpak.elementary.io/repo.flatpakrepo)
• PureOS Flatpaks – (https://store.puri.sm/repo/stable/pureos.flatpakrepo)
• EndlessOS Flatpaks – (https://ostree.endlessm.com/ostree/eos-apps)

That being said, I didn’t find these other repos very user-friendly. They didn’t have a browsable list for me to discover what’s available. Most users should probably stick to Flathub for now.

Building Your Own Flatpak Application

What if you want a desktop program that isn’t available on Flathub yet?
In that case, you can manually package a program into a Flatpak yourself.

You’ll need to create a manifest, which is a text file, to define your Flatpak app. The hardest part is figuring out which runtime and SDK to specify to make your program work. For more information, see the official documentation on building your first Flatpak.

Truthfully, this is for advanced users and requires testing, so I wouldn’t recommend jumping into this process unless you absolutely need something you can’t get through other means (such as a specific program for an embedded system with Apertis).

Using Flatpak: Common Tasks

Now that you’ve found the apps you want, how do you actually install them? In this section, I’ll give you a quick guide to the most common commands for Flatpak on Raspberry Pi OS.

Installing Flatpak Apps

Unfortunately, there’s no official way install Flatpak apps on Raspberry Pi OS directly from the GUI. For now, you can install them via the command line, using a syntax that’s similar to APT.

Search for a Flatpak app: flatpak search <phrase>
flatpak search comic

From the search results, you can get the “Application ID,” which is what you need to install it.

Install a Flatpak app: flatpak install <source> <appID>
flatpak install flathub app.opencomic.OpenComic

You can add sudo in front of the command if you don’t like having to enter your password multiple times.

Personally, I find it easier to browse through Flathub and copy/paste the installation command from there:

List all installed Flatpaks:
flatpak list

Uninstall a specific Flatpak app: flatpak uninstall <appID>
flatpak uninstall org.gimp.GIMP

Note: Although it’s unofficial, there’s a Flatpak graphical tool that seems to work for Raspberry Pi OS. You can try it out by installing Warehouse:
flatpak install flathub io.github.flattool.Warehouse

Running Flatpak Apps

After installing a Flatpak app, it’ll probably appear under the Raspberry Pi OS main menu. In my case, I had to wait a few minutes for the menu to refresh. You can also reboot as a last resort.

Alternatively, you can launch the app manually from the terminal: flatpak run <appID>
flatpak run app.opencomic.OpenComic

If Raspberry Pi OS didn’t create a shortcut for you, you could always create a desktop shortcut manually.

Updating Flatpak Apps

Flatpak lets you update each app independently, meaning it won’t affect any other packages on your system. This is especially handy if stability is important to you on your Raspberry Pi.

Update a specific app only:
flatpak update <appID>

Update all Flatpak apps:
flatpak update

Managing Flatpak Repositories

You have full control over which Flatpak repositories you want on your system (though most people will probably use Flathub).

View sources:
flatpak remotes

Add a new source: flatpak remote-add –if-not-exists <repo_name> <repo_link>
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

Remove a source: flatpak remote-delete <repo_name>
flatpak remote-delete flathub

For a complete list of other commands, check out the official documentation.

Final Thoughts: Pros & Cons of Flatpak

Here’s a quick summary to help you decide if Flatpak is right for your needs:

Pros	Cons
All-in-one packages.	Programs require more memory to run.
Simplifies installation.	Uses extra disk space compared to APT.
Security through sandboxing.	Many apps break out of their sandbox anyway.
Apps can run without admin privileges.	File permission issues.
Great for desktop applications.	Not meant for command-line programs.

When to Use Flatpak

In short, Flatpak is great when you want a graphical app that requires a lot of steps to install on Raspberry Pi OS, or you can’t get it running on the desktop because the app requires admin privileges.

Flatpak is also handy if you need an application to be standalone and updated separately from all other dependencies on the system.

When Flatpak Isn’t the Best Choice

Flatpak is probably not the right choice for a headless server or for command-line applications.

Let’s go over some of the downsides:

• Higher resource usage: Flatpak bundles everything necessary for each app to function independently; each app uses more RAM and disk space than when installing something the default way with APT.
  
• Security concerns: I don’t think Flatpak is as secure as claimed. Sure, Flatpak creates containers that are restricted from the rest of your system, but graphical programs have to integrate with your desktop environment and user files to function. So in practice, they’re often configured to break out of their sandbox anyway. Also, some packages are not published by the original developers, so you’ll have to be more vigilant about what you install.
  
• File permission issues: There can be file permission issues due to the sandbox design, making it so some apps can’t see the files you need for it to work the way you want. When running the Flatpak version of Minecraft, I run into all sorts of conflicts when trying to get mods or resource packs working. There are probably ways to fix it, but it’s rather finicky.

Bottom line
Overall, I still think Flatpak has a lot of merits as a package manager on Raspberry Pi OS. I hope that Flatpak helps you discover a whole new world of programs for your Raspberry Pi!

If you’re curious about other ways to install programs on Raspberry Pi OS, don’t forget to check out our articles below:

• How to Easily Install Apps on Raspberry Pi OS? (5 Methods)
• 7 Useful Linux Commands to Install and Manage Software

Whenever you’re ready, here are other ways I can help you:

Test Your Raspberry Pi Level (Free): Not sure why everything takes so long on your Raspberry Pi? Take this free 3-minute assessment and see what’s causing the problems.

The RaspberryTips Community: Need help or want to discuss your Raspberry Pi projects with others who actually get it? Join the RaspberryTips Community and get access to private forums, exclusive lessons, and direct help.

Master your Raspberry Pi in 30 days: If you are looking for the best tips to become an expert on Raspberry Pi, this book is for you. Learn useful Linux skills and practice multiple projects with step-by-step guides.

Master Python on Raspberry Pi: Create, understand, and improve any Python script for your Raspberry Pi. Learn the essentials step-by-step without losing time understanding useless concepts.

You can also find all my recommendations for tools and hardware on this page.