Flatpak apps (flatpak)

The flatpak manager installs Flatpak apps and runtimes into the system-wide installation, and flatpak-user installs them for the current user. Both use the flatpak command.

[bootstrap.packages]
"flatpak:org.mozilla.firefox" = "latest"
"flatpak-user:org.gnome.Builder" = "latest"

mise bootstrap packages apply --manager flatpak --dry-run
mise bootstrap packages apply --manager flatpak
mise bootstrap packages apply --manager flatpak-user

Prerequisites

Both managers are available on Linux when flatpak is on PATH. On other machines, their entries show as skipped. mise does not install Flatpak or configure remotes, so add a remote such as Flathub in the scope you use before you apply.

For system-wide apps:

flatpak remote-add --system --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
mise bootstrap packages use flatpak:org.mozilla.firefox

For your user only:

flatpak remote-add --user --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
mise bootstrap packages use flatpak-user:org.gnome.Builder

A remote added in one scope is not available to the other. Check with flatpak remotes --system or flatpak remotes --user.

mise does not run Flatpak with sudo. System-wide changes go through Flatpak's own polkit authorization, which can prompt in a desktop session. Where no one can answer that prompt, run mise as root or use flatpak-user, which needs no authorization.

Package names

Use the app or runtime ID that flatpak install takes, such as org.mozilla.firefox. The two scopes are separate, so a config can declare the same ID in both. When several remotes provide an ID, resolve the ambiguity in Flatpak's configuration; a declaration cannot name a remote.

Installed apps get no mise shims. Start them from the desktop, or with flatpak run org.mozilla.firefox.

Version pins

Flatpak cannot install a specific older version through flatpak install, so mise cannot install a pin. A pinned entry shows as version mismatch while another version is installed, and apply and upgrade skip it with a warning. Use "latest".

What mise runs

Operation	Command
Check installed state (no sudo)	flatpak list --system --columns=application,version
Install	flatpak install --system --noninteractive <ids>
Upgrade	flatpak update --system --noninteractive <ids>

flatpak-user runs the same commands with --user in place of --system. apply --update has no effect for Flatpak.

Remove packages

mise does not remove Flatpak apps. Deleting an entry leaves the app installed; run flatpak uninstall yourself.