Setting Up Flatpak and Flathub on elementary OS for Extra Apps
elementary OS ships with AppCenter, a curated storefront that prioritises quality over quantity. For many people, that's exactly the point: a tight selection of polished native and packaged applications, an opinionated design philosophy, and a system that feels coherent out of the box. The downside is that some genuinely useful software simply isn't included, and waiting for an elementary-specific build can drag on for months, especially for niche tools or recent upstream releases. That's where Flatpak and Flathub come in. Flatpak is a universal sandboxed packaging format that lets you install software across distros without messing with the underlying system, and Flathub is the largest public repository of Flatpak apps on the web.
If you're setting this up from a fresh install on Pantheon, the process is refreshingly short, but a couple of preparatory steps make it smoother. Flatpak itself is already installed by default on recent elementary OS releases, so you mainly need to add the Flathub remote and decide whether you want a graphical front-end. The rest of this walkthrough covers that process, points out a few quirks specific to Pantheon, and shares some troubleshooting tips that have saved me a fair bit of faffing about.
Why Flatpak is worth setting up on elementary OS
Flatpak solves a genuine problem for everyday users. The elementary team maintains a small but carefully selected catalogue, and they're not afraid to say no to apps that don't meet their standards. That's lovely if you're a designer or someone who values curation, but it leaves gaps. A musician in Adelaide trying to install a specific LV2 plugin host, a video editor in Brisbane waiting for an upstream release, or a researcher in Hobart who needs a particular scientific tool may find nothing equivalent in AppCenter. Flathub fills those gaps with thousands of community-published packages that run in their own sandboxed environments.
There's a real benefit to this sandboxing beyond simply having more software. Each Flatpak app runs with a tightly scoped set of permissions, so a media player doesn't need access to your entire home directory or your SSH keys. For anyone who has ever felt uneasy installing random .deb files from the internet, this containment is a genuine improvement. It also makes it easier to roll back an application or remove it cleanly without leaving stray dependencies behind. Combined with Pantheon's already restrained approach to background services, Flatpak apps feel like a natural extension of the elementary philosophy rather than a contradiction of it.
One practical wrinkle for Australian users is bandwidth. Many of the bigger Flatpak runtimes are a few hundred megabytes, and some apps pull in additional SDK extensions on top of that. On a solid NBN connection in the suburbs, that's a non-issue, but if you're on a slower rural Sky Muster Plus plan or you're rationing your mobile data during a long train ride between Sydney and Melbourne, you might want to schedule the first install for when you're on a decent connection. Once the runtimes are cached, subsequent app installs are tiny.
Preparing your system before you start
Before touching anything, make sure your system is up to date. Open the Terminal app from the Applications menu and run the usual update sequence. You'll need sudo privileges, and you'll be prompted for your password. If you're not familiar with the command line, the same job can be done through AppCenter's update tab, but the terminal route is faster and gives you clearer feedback when something stalls.
You should also check which version of elementary OS you're running, because the exact steps differ slightly between releases. The Settings panel shows this under About, and you can also grab it from the terminal with a quick command. Knowing your version helps when you run into documentation written for an older release, and it saves you from following a tutorial that no longer applies.
Take a moment to back up anything important. Flatpak is generally safe, but if you've heavily customised AppCenter's settings, or you've installed a lot of third-party .deb packages, a Timeshift snapshot can save your bacon if something goes sideways. The relevant build of Timeshift is available directly from AppCenter or via Flathub itself, so there's no need to hunt around for a separate download.
Adding the Flathub remote
With the system updated and a backup in place, the next step is to tell Flatpak about the Flathub repository. The Flathub team publishes an official one-liner that downloads a small configuration file and registers the remote with the appropriate GPG key. It's clean, signed, and avoids the kind of half-broken instructions you sometimes see in older forum posts floating around the Australian Linux community.
Run that command in your terminal and confirm the prompt. Within a couple of seconds, Flatpak will know where to fetch apps from. You can verify it's working with a quick search, which will list available applications from the new remote. If you see a long list of app names scroll past, you're in business.
A common gotcha is corporate or institutional networks that intercept HTTPS traffic or block third-party package sources. Universities in Australia occasionally filter Flathub, and some shared office Wi-Fi setups have similar restrictions. If your command hangs or returns a TLS error, try again on a different network, such as a personal hotspot or home broadband. The Flathub infrastructure itself is robust and rarely the actual problem.
Installing apps from the terminal
Once Flathub is added, installing apps is a single command. You search for the app you want, copy its application ID, and pass it to the install command. Flatpak then resolves any required runtimes and dependencies, downloads everything, and wires up a launcher entry in Pantheon. The whole process feels much like installing software on a phone, with the sandboxing handled for you.
For multimedia work, this is where Flatpak really shines. Tools like Kdenlive, OBS Studio, Ardour, and Audacity all have current Flatpak builds on Flathub, and they tend to track upstream releases closely. If you're into music production or video editing and you've been frustrated waiting for a native elementary package, the Flathub versions are well worth a look. There's a handy roundup of recommended picks over at the multimedia applications page on elementarynow, which lists a few favourites alongside install commands.
A few flags make the experience smoother. --user installs apps to your home directory rather than system-wide, which is useful if you don't have admin rights on a shared machine or if you simply want to keep your install self-contained. --assumeyes skips the confirmation prompt, which is handy for scripted setups. And flatpak update keeps everything current, including the runtimes that multiple apps share.
Using a graphical front-end for browsing
Not everyone wants to live in the terminal, and that's perfectly fine. elementary OS doesn't include a built-in graphical Flatpak browser, but you can add one. The most common approach is to install GNOME Software with the Flatpak plugin, which gives you a familiar store-style interface for browsing and installing apps. It integrates reasonably well with Pantheon, though the visual style doesn't match the rest of the system.
If you'd rather keep things lean, Sideload is a small dedicated Flatpak browser designed for elementary OS in particular. It uses the same minimalist aesthetic as the rest of the desktop and focuses on doing one thing well. It won't replace AppCenter, and it doesn't aim to. It's a complementary tool for the apps that AppCenter doesn't carry.
Whichever route you pick, the apps you install will appear in the Applications menu alongside your native software. They run in their own sandboxed environments but feel responsive and integrated, with full access to your files when you grant them permission. For an Australian user setting up a family PC or a small office workstation, this hybrid approach often hits the sweet spot: the curated store for everyday software, Flatpak for everything else.
Managing permissions, runtimes, and updates
Flatpak's permission system is one of its quiet superpowers. Each app has a manifest declaring what it needs, and you can override those defaults using a tool called Flatseal. If you want to give a particular app access to a specific folder, a USB device, or a network socket, Flatseal lets you do that without touching config files. It's the kind of tool that grows on you once you start using it, especially if you're juggling a few specialised apps.
Runtimes are the shared base layers that Flatpak apps sit on top of. They're cached on your system and updated independently of the apps themselves. From time to time, you'll see a prompt to install a new runtime version. There's no harm in saying yes, but if you're tight on disk space, you can prune older runtimes with a single command. Many Australian users on laptops appreciate this, especially if they're running on a smaller SSD and don't want bloat piling up.
Updates work just like native packages. Flatpak checks for new versions in the background, and you can trigger an update manually whenever you like. Apps installed with --user only update when you're logged in as that user, which is handy on shared machines. For a fully managed setup, you can even automate updates with a small systemd timer or a cron job, which suits anyone running a fleet of machines for a local business or community group.
Troubleshooting common hiccups in Australia
A few issues crop up regularly. The first is theme integration. Some Flatpak apps ship with their own toolkit styles and don't pick up the elementary or Adwaita theme by default, which makes them look out of place. Installing a couple of theme packages from Flathub usually fixes this. There's also an environment variable you can set to force a consistent dark or light mode across apps that respect it, useful when you're working late and don't want a blinding white window.
Another common complaint is slow startup on older hardware, particularly laptops that have seen a few summers of Australian heat. If your machine is throttling or the fan is constantly loud, Flatpak apps can feel sluggish because of the extra sandboxing layer. Closing a few background tabs, ensuring adequate ventilation, and avoiding stacked resource-heavy apps will help. For persistent thermal issues, a can of compressed air and a clean desk go a long way.
Finally, if you ever need to start fresh, removing a Flatpak app is just as easy as installing one. The app itself, its data directory, and any unused runtimes can all be cleaned up with a couple of commands. Should Flathub become unreachable, or you simply want to roll back your setup to a stock elementary install, a full uninstall leaves no trace behind. That reversibility is one of the most underrated features of the whole system, and it means there's no real risk in trying Flatpak out to see if it fits your workflow before fully committing to it as part of your daily setup.
