In this tutorial, we will explain how Flatpak consumes disk space and the effective commands and techniques to remove unused flatpak apps to reclaim that space.
Table of Contents
TL;DR
The main commands to clean up unused flatpak apps are:
flatpak uninstall --unusedto remove runtimes and extensions no longer needed by any installed app.flatpak repairto fix corrupted or inconsistent objects and remove invalid data.flatpak remove --delete-data --unusedto also purge per-app user data that’s orphaned.
Beyond that, you can clear AppStream metadata caches and manually prune leftover object files.
Understanding Flatpak Apps Disk Usage
Flatpak apps run in sandboxes and bundle all libraries they need, which leads to larger disk usage than traditional packages.
Each update may download a full new version of a runtime or extension, then keep the old one around until explicitly removed.
Runtimes (like org.gnome.Platform or org.kde.Platform) are shared by multiple apps, so stale versions accumulate over time if not cleaned.
To understand more about Flatpak disk usage, please visit the following link:
Checking Flatpak Disk Usage
Flatpak stores each application along with its runtimes and extensions in per-user (~/.local/share/flatpak) and system (/var/lib/flatpak) repositories, often leaving unused runtimes behind after updates or uninstalls.
You can inspect how much space Flatpak is using the following commands:
du -sh ~/.local/share/flatpak du -sh /var/lib/flatpak
Or list installed runtimes by size:
flatpak list --runtime --columns=application,size
Sample Output:
--columns=application,size Application ID Installed size org.freedesktop.Platform 604.3 MB org.freedesktop.Platform 675.7 MB org.freedesktop.Platform.GL.default 538.1 MB org.freedesktop.Platform.GL.default 538.1 MB org.freedesktop.Platform.GL.default 463.3 MB org.freedesktop.Platform.GL.default 463.3 MB org.freedesktop.Platform.VAAPI.Intel 46.9 MB org.freedesktop.Platform.VAAPI.Intel 51.8 MB org.freedesktop.Platform.ffmpeg-full 30.4 MB org.freedesktop.Platform.openh264 763.9 kB org.freedesktop.Platform.openh264 789.5 kB org.gimp.GIMP.HEIC 8.1 MB org.gnome.Platform 1.0 GB org.gnome.Platform 1.0 GB
This helps identify unusually large runtimes or apps.
Removing Unused Flatpak Runtimes and Extensions
Remove all runtimes and extensions no longer required:
flatpak uninstall --unused
This is equivalent to an “autoremove” for Flatpak and can free gigabytes if you haven’t run it in a while.
Purge Orphaned App Data
To also delete user-specific data for uninstalled apps:
flatpak remove --delete-data --unused
This clears out ~/.var/app/<app-id> directories that otherwise linger, reclaiming additional space.
Repairing and Pruning Corrupt or Leftover Files
Fix any broken or inconsistent objects; this can remove invalid files:
flatpak repair # and for per-user installations flatpak --user repair
This scans for and deletes any orphaned or corrupted objects.
Clear AppStream Caches
Flatpak maintains AppStream metadata under:
~/.local/share/flatpak/appstream//var/lib/flatpak/appstream/
You can safely remove these caches; they will be regenerated on next update:
rm -rf ~/.local/share/flatpak/appstream/* sudo rm -rf /var/lib/flatpak/appstream/*
This can free dozens of megabytes and speeds up metadata queries.
Manual Cleanup of Object Repositories
Sometimes /var/lib/flatpak/repo/objects or ~/.local/share/flatpak/repo/objects holds data from fully uninstalled apps. After confirming you’ve uninstalled everything you don’t need, you can remove these directories entirely:
sudo rm -rf /var/lib/flatpak/repo/objects rm -rf ~/.local/share/flatpak/repo/objects
Flatpak will recreate them as needed, and you’ll reclaim any leftover blocks.
Automating Regular Cleanup
To avoid future bloat, add a cron job or systemd timer to run cleanup weekly:
sudo nano /etc/cron.weekly/flatpak-clean
Add the following contents in it:
#!/bin/sh
flatpak uninstall --unused -y
flatpak remove --delete-data --unused -y
flatpak repair -y
Make it executable:
sudo chmod +x /etc/cron.weekly/flatpak-clean
This keeps your Flatpak footprint minimal.
Please note that the scripts placed in /etc/cron.weekly/ are executed by the cron daemon on a weekly basis. The exact day and time can vary depending on your system's configuration.
Scripts in /etc/cron.weekly/ are executed as the root user. So just make sure that the commands within the script are safe to run with elevated privileges.
Cheat Sheet
| Action | Command |
|---|---|
| Remove unused runtimes & extensions | flatpak uninstall --unused |
| Purge orphaned app data | flatpak remove --delete-data --unused |
| Repair installation | flatpak repair``flatpak --user repair |
| Clear AppStream caches | rm -rf ~/.local/share/flatpak/appstream/*``sudo rm -rf /var/lib/flatpak/appstream/* |
| Manual prune of object repos | sudo rm -rf /var/lib/flatpak/repo/objects``rm -rf ~/.local/share/flatpak/repo/objects |
Following these steps will typically recover anywhere from a few hundred megabytes to multiple gigabytes of space, depending on how long you’ve let Flatpak runtimes accumulate without pruning.
