Why I sometimes choose Flatpak over native packages
As a Linux user, I’ve always appreciated the ease, control and relative safety that comes with package managers like apt, or dnf. Native packages are optimised for my distribution, they mostly integrate well with the system, and generally feel like the “right” way to install software on the Linux desktop.
But over time, I’ve found myself testing out Flatpak applications more and more — especially for certain apps. For example, I use the Flatpak version of Calibre. Why? Simple — the Flatpak version is currently 8.4.0 versus version 5.37.0 on Linux Mint 21.3 (which pulls from Ubuntu Jammy). It has never been clear to me as to why the gulf between the two is so large; I don’t really care to be honest! I just want to use the latest version of this particular application and enjoy the new features available in version 8.
Similarly, GIMP is currently version 2.10.30 via apt whilst I’ve been enjoying version 3 since March 2025. I could easily upgrade to Linux Mint 22 to access a more resent version or — better yet — add a third-party PPA to upgrade to version 3 for GIMP. But that’s a lot of bother so, Flatpak!
Generally, I’m not looking to have “bleeding edge” everything when it comes to my system and software; there’s Fedora for that and I don’t use Fedora anymore. However, on the rare occasion, I would like to get early access to the latest version of an application. Or at least a more recent version than the one available via my distribution.
My criteria for sometimes going with Flatpak are:
- to get rid of bugs which annoy me
- to have access to new features which would improve my personal workflow
- to sometimes gain access to an application itself.
The Flatpaks currently installed on my desktop are:
- Calibre
- Flatseal
- GIMP
- Upscaler
Upscaler is simply not available anywhere else and I use this tool a lot. So, again, Flatpak! Certainly, I can build the app myself and install it that way but…let’s not get too nerdy!
The sandboxing question
I’m crystal clear on one point: Applications installed from package managers like aptor dnf typically come without any sandboxing. Flatpak apps run in a sandbox, which restricts their access to my system by default. While not all apps enforce strict confinement, the model itself is arguably a security improvement over traditional packages.
Flatpak application permissions can easily be checked and tweaked by using Flatseal, for example. With Flatseal, I can restrict each application’s system access as needed and also, spot any delinquent apps by checking what permissions they install with. Why would GIMP need access to my webcam, as an example? It doesn’t but if it did have permissions, I would know from checking with Flatseal.
I still prefer native packages
Flatpak isn’t always the best choice. For system utilities, or performance-critical software (like games or drivers), I 100% stick with native packages. Flatpak’s sandboxing can add overhead (think greater storage space or slow install/update/startup times), and some apps just work better when deeply integrated into the base system.
For me, the most significant advantage of using Flatpak is that I have access to the latest versions of applications. Traditional package managers may hold back updates to ensure system stability, so I use Flatpak instead of waiting for my distribution to catch. Flatpak allows me to enjoy the latest features, bug fixes, and performance improvements. And that’s why.