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Created: September 18th 2025
Categories: IT Knowledge,  IT Support,  Linux,  Operating Systems
Author: Dusan Rasic

Flatpak vs APT in Linux Mint – Full Comparison and Practical Guide

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Introduction

Linux Mint is one of the most user-friendly Linux distributions available today. It’s stable, intuitive, and built to make the transition from Windows as smooth as possible. One of the first things every user notices in Linux Mint is the way software is installed and updated. Unlike Windows, where you mostly download installers from websites, Mint offers centralized software management through package managers.

But here comes a common question: should you use APT or Flatpak in Linux Mint? The answer depends on your needs. In this guide, we’ll explain the differences in detail, highlight real-world examples, and help you decide which tool is best for your workflow. By the end, you’ll have a clear understanding of when to stick with APT and when to embrace Flatpak.

What is APT?

APT (Advanced Package Tool) is the traditional package manager used by Debian, Ubuntu, and Linux Mint. It pulls software directly from official repositories that are tested and maintained by the Linux Mint and Ubuntu teams. When you install something using APT, you know it has been reviewed for stability and compatibility with your Mint version.

  • Source: Official repositories (Mint, Ubuntu, Debian)
  • Updates: Come with your regular system updates
  • Integration: Seamlessly tied to the operating system
  • Performance: Lightweight and optimized for your system

APT has been around for decades, and it’s extremely reliable. Most Linux guides, tutorials, and forums assume you’re using APT when they tell you to “run this command to install X.”

What is Flatpak?

Flatpak is a newer approach to software distribution that aims to make apps universal across different Linux distributions. Instead of relying on the Mint repositories, Flatpak apps usually come from Flathub, a large community-driven app store. Flatpak apps are sandboxed, meaning they run in isolation from your system, which adds an extra layer of security.

  • Source: Flathub or other Flatpak repositories
  • Updates: Managed separately from system updates
  • Integration: Runs in a sandbox, isolated from your system
  • Flexibility: Often provides the very latest app versions

Flatpak is especially useful for modern desktop apps that move fast, such as Spotify, Zoom, or Visual Studio Code, where the Flatpak version is updated far more frequently than the APT version.

Key Differences Between APT and Flatpak

While both APT and Flatpak let you install and manage software, they work differently under the hood. Here’s a comparison table that highlights the main differences:

Feature APT Flatpak
App Versions Stable, but often older Latest versions available
System Integration Full integration with Mint Isolated, sandboxed
Security Relies on system-level updates Enhanced with sandboxing
Storage Usage Minimal footprint Heavier due to runtimes
Best For Core apps and stability Latest apps and new features

Practical Examples

Example 1: Installing GIMP

If you install GIMP via APT, you might get version 2.10.x, which is stable but not the absolute latest. If you install via Flatpak, you’ll likely get the newest release, possibly 2.99.x (development build).

# APT version
sudo apt install gimp

# Flatpak version
flatpak install flathub org.gimp.GIMP

Example 2: Zoom

Zoom is not in the APT repositories by default. You’d need to manually download a .deb file. But with Flatpak, it’s just:

flatpak install flathub us.zoom.Zoom

Example 3: Mixing Both

You can have an app installed via both APT and Flatpak at the same time. This is handy if you want to compare performance or test features. For instance, run the APT-installed GIMP for stability, but also keep the Flatpak version for testing new tools.

How to Check Which Version You’re Running

Sometimes you might forget which package manager you used. Here’s how to check:

  • APT apps: Installed in /usr/bin/ and managed via dpkg
  • Flatpak apps: Installed under /var/lib/flatpak/ or ~/.local/share/flatpak/

You can also run:

which gimp
flatpak list | grep gimp

Performance Considerations

Flatpak apps can sometimes feel a little slower to start because of sandboxing and additional runtimes. They also use more disk space, since each app may include its own libraries. APT apps, on the other hand, share system libraries, which keeps them smaller and more efficient.

If you’re using an older laptop with limited storage or RAM, APT is usually the better choice. If you’re on a modern system and prefer having the newest features, Flatpak is worth it.

Security Aspects

One major advantage of Flatpak is sandboxing. Apps have restricted access to your system, which reduces the chance of malware or accidental system damage. However, keep in mind that Flatpak permissions can be customized. Tools like Flatseal let you fine-tune app permissions (such as access to files, USB devices, or the internet).

APT apps are not sandboxed, but they are thoroughly tested and vetted by Mint/Ubuntu developers. Security updates are pushed regularly through the Mint Update Manager.

Storage Usage: The Hidden Cost of Flatpak

One thing users often notice is that Flatpak apps take up more disk space. For example:

  • APT GIMP: ~150 MB
  • Flatpak GIMP: ~800 MB (with runtimes)

This is because Flatpak apps bundle extra runtimes to ensure compatibility across all Linux distros. While this makes Flatpak universal, it does come with a storage cost.

When Should You Use APT?

  • For system-level tools (drivers, system utilities)
  • When you value stability and long-term support
  • If you’re low on storage and want smaller apps

When Should You Use Flatpak?

  • When you want the latest version of a desktop app
  • If an app is missing from the APT repositories
  • When you need better security isolation

Tips for Using Both Together

Linux Mint supports both systems side by side, so there’s no need to choose one permanently. Some tips:

  • Prefer APT for system-critical apps
  • Use Flatpak for modern apps where you want the newest features
  • Be mindful of duplicates: uninstall one version if you don’t need both
  • Check disk space regularly if you install many Flatpak apps

Conclusion

Flatpak and APT are not competitors but complementary tools in Linux Mint. APT gives you rock-solid stability and integration, while Flatpak provides flexibility and cutting-edge software. By understanding when to use each, you can make the most of your Mint experience.

For everyday users, the best approach is simple: use APT for your core apps and Flatpak for your modern apps. This way, you get the perfect balance of stability and freshness without sacrificing performance.

Final Thoughts

Linux Mint’s decision to support both package managers is one of the reasons it’s so popular among Linux users. You’re not locked into one ecosystem—you get the freedom of choice. So the next time you install an app, ask yourself: do I want stability, or do I want the latest features? The answer will guide you to APT or Flatpak.

Whichever you choose, you’ll be building a Linux Mint system that’s tailored to your needs, reliable for work, and flexible for fun.