How To Fix Broken Flatpak Issue In Ubuntu 25.10 Questing Quokka

If you’ve recently upgraded (or fresh-installed) Ubuntu 25.10 “Questing Quokka” and found that your favourite Flatpak apps (from Flathub or elsewhere) are failing to install or update — you’re not alone. This post explains what’s wrong, why it happened, and how you can fix it now, as well as what to watch for in terms of the official fix.

What’s the problem?

After the release of Ubuntu 25.10, many users encountered an error when installing or updating Flatpak-based applications. A typical message might look like:

Warning: Could not unmount revokefs-fuse filesystem at /var/tmp/flatpak-cache-…: Child process exited with code 1  
error: Failed to install org.gnome.Platform: Could not unmount revokefs-fuse filesystem …

(OSTechNix)

In short: Flatpak installations and updates broke. (OMG! Ubuntu)

Why did it happen?

The root cause is linked to the system’s security module, AppArmor. Here’s the breakdown:

Flatpak uses FUSE (filesystem in user-space) to mount/unmount parts of the sandboxed environment of an app. That means tools like fusermount3 get invoked behind the scenes. (OSTechNix)
In Ubuntu 25.10, the AppArmor profile for fusermount3 lacked certain privileges — specifically, access to files like /run/mount/utab and related files. Because of this, the unmount operation failed and the Flatpak operation was aborted. (It’s FOSS News)
The bug was flagged as critical by the Ubuntu developers/maintainers. (It’s FOSS News)

So: it’s not a problem with your Flatpak repository or your app per se — it’s a system-level security profile that is blocking required steps.

How to fix it NOW (workarounds until the official update arrives)

While waiting for the official fix, you can apply one of the following workarounds. Note: These are temporary and one of them reduces your system’s security protections slightly — remember to revert or update when the fix is applied.

✅ Method A – Disable the AppArmor profile for `fusermount3`

Link the profile into the disable directory:
sudo ln -s /etc/apparmor.d/fusermount3/etc/apparmor.d/disable/
Unload the profile from the kernel:
sudo apparmor_parser -R /etc/apparmor.d/fusermount3
Now try installing or updating your Flatpak apps again. In many cases this will restore functionality. (OSTechNix)

Note: This method turns off the AppArmor profile for fusermount3, which reduces the sandboxing/security checks for mounts/unmounts. Use with caution.

✅ Method B – Use `sudo` to install Flatpaks system-wide

If you prefer not messing with AppArmor profiles:

sudo flatpak install flathub <app-ID>

By installing as root (with sudo), you may bypass the user-level AppArmor restrictions causing the failure. (OSTechNix)

✅ Method C – Wait and update

There is an official fix in the works (and already released into testing). Consider holding off heavy Flatpak usage until your system receives it.

Official permanent fix: What’s coming

Good news: The Ubuntu developers have already addressed this bug. Key details:

They updated the AppArmor profile to allow fusermount3 additional permissions (including access to /run/mount/utab.lock rwk, among others). (OSTechNix)
The fix appears in AppArmor version 5.0.0~alpha1-0ubuntu8.1 (or newer) in Ubuntu’s proposed/testing repository. (OSTechNix)
Once the update is released to the stable channel, you should re-enable the AppArmor profile (if you disabled it) so your system returns to full protection. (OSTechNix)

How to re-enable after update:

sudo rm /etc/apparmor.d/disable/fusermount3
sudo apparmor_parser -a /etc/apparmor.d/fusermount3

Once the fixed package is installed and profile re-loaded, your Flatpak installations should work without any further workarounds.

Step-by-step: What I’d do if I were you

Check if you are affected
Try installing or updating a Flatpak app. If you get the “Could not unmount revokefs-fuse filesystem” error, you’re impacted.
(OSTechNix)
Apply workaround
Choose either Method A or Method B above. If you’re comfortable with AppArmor, Method A will give full functionality. If you prefer minimal changes, Method B will suffice.
Monitor updates
Run sudo apt update && sudo apt upgrade periodically. Once the AppArmor updated version lands, install it.
Re-enable profile (if you disabled it)
As mentioned above, restore the fusermount3 AppArmor profile.
Test Flatpak again
Install/update a Flatpak app. If successful without error, issue resolved.
Keep an eye on Ubuntu’s bug tracker / release notes
The fix is in the queue, and you’ll want to ensure you stay on top of any other side-effects.

Final thoughts

It’s frustrating to face a bug like this immediately after upgrading to Ubuntu 25.10 — especially one that affects so many users and a popular packaging format like Flatpak. But the good news is: it’s not you — it’s a known issue, and it’s been addressed.

If you rely heavily on Flatpak apps, I’d recommend applying the workaround now (especially if you need immediate functionality). Just remember to revert your workaround after the official fix lands so your system retains full security.

Mark Vincent

Tech enthusiast and content creator passionate about making technology simple for everyone. I share practical tips, guides, and reviews on the latest in computers, software, and gadgets. Let’s explore the digital world together!