Flatpak installs sandboxed desktop applications from remotes such as Flathub—Firefox, Steam, GIMP, and thousands of others—without mixing their dependencies into APT. On Debian, you install the flatpak package from main, add the Flathub remote once, then run flatpak install (official Debian setup, Debian Wiki — Flatpak).
This guide covers install Flatpak on Debian for Debian 11 (Bullseye), 12 (Bookworm), and 13 (Trixie): install flatpak, configure Flathub, install apps (system or user scope), optional GNOME Software integration, update, and uninstall. I ran these steps on Debian 13 and kept real terminal output below. For apps you can also install through other channels, see install Firefox on Debian and install Steam on Debian.
Tested on: Debian 13 (trixie); kernel 6.12.94+deb13-amd64; amd64; Flatpak 1.16.6; Flathub remote; sample apps Flatseal 2.4.1 (system), Spider 0.0.7 (user).
.deb packages—apt list --installed does not show them. Use flatpak list alongside list installed packages on Debian for a full software inventory.
Choose an install path
| Step | Purpose | On test host |
|---|---|---|
apt install flatpak |
Flatpak CLI and system integration | 1.16.6-1~deb13u1 |
| Add Flathub remote | Application catalog (flathub.org) | flathub remote |
flatpak install flathub APP |
Install sandboxed apps + runtimes | Flatseal, Spider |
gnome-software-plugin-flatpak (optional) |
Install/update Flatpaks in GNOME Software | Available in apt, not required |
There is no separate flatpak third-party repository for current Debian releases—flatpak comes from Debian main on Bookworm and Trixie.
Flatpak on Debian releases
| Debian | Codename | Typical source |
|---|---|---|
| 13 | trixie |
apt install flatpak (main) |
| 12 | bookworm |
apt install flatpak (main) |
| 11 | bullseye |
flatpak in bullseye-backports for newer releases (Debian Wiki) |
Check what is installed
. /etc/os-release && echo "$PRETTY_NAME"
command -v flatpak || echo "flatpak: not installed"
flatpak --version 2>/dev/null
flatpak remote-list 2>/dev/null
dpkg -l flatpak 2>/dev/null | grep ^iiBefore install on the test host:
Debian GNU/Linux 13 (trixie)
flatpak: not installedAfter apt install flatpak:
Flatpak 1.16.6
flathub system
ii flatpak 1.16.6-1~deb13u1 amd64 Application deployment framework for desktop appsPrerequisites
- Debian 11, 12, or 13 on amd64 or arm64 with a desktop session (GNOME, KDE, Xfce, etc.) for GUI apps.
- sudo for system-wide installs and the
flatpakpackage. - Outbound HTTPS to
deb.debian.organddl.flathub.org. - xdg-desktop-portal (often pre-installed on desktops) so sandboxed apps can open files and URLs—
xdg-desktop-portal-gtkon GTK desktops.
dpkg -l xdg-desktop-portal xdg-desktop-portal-gtk 2>/dev/null | grep ^iiii xdg-desktop-portal 1.20.3+ds-1
ii xdg-desktop-portal-gtk 1.15.3-1Disk space: a single app plus runtimes used about 1.7 GB under /var/lib/flatpak on the test host—plan more for games or IDEs.
Install Flatpak from Debian apt
Per flatpak.org — Debian:
sudo apt update
sudo apt install -y flatpakSelecting previously unselected package flatpak.
Unpacking flatpak (1.16.6-1~deb13u1) ...
Setting up flatpak (1.16.6-1~deb13u1) ...Verify:
flatpak --version
which flatpakFlatpak 1.16.6
/usr/bin/flatpakLog out and back in (or reboot) after the first install if your desktop’s app menu does not show new Flatpaks—Flathub’s Debian notes mention this for some sessions.
Add the Flathub remote
Flathub is the default application store for Flatpak:
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak remote-listflathub systemSearch before installing:
flatpak search firefox | head -3Firefox Fast, Private & Safe Web Browser org.mozilla.firefox 152.0.3 stable flathubInstall Flatpak applications
System-wide install (all users)
Use sudo so apps land in /var/lib/flatpak:
sudo flatpak install -y flathub com.github.tchx84.Flatseal
flatpak list --appFlatseal com.github.tchx84.Flatseal 2.4.1 stable systemFlatseal is a small permissions manager—useful for testing Flatpak without downloading a large browser.
Per-user install
For installs under ~/.local/share/flatpak without root:
flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak install --user -y flathub io.github.zaedus.spider
flatpak list --userSpider io.github.zaedus.spider 0.0.7 stableflatpak install --user reports No remote refs found for 'flathub', you added Flathub only at system scope. Run flatpak remote-add --user as shown above.
Examples: Firefox and Steam
sudo flatpak install -y flathub org.mozilla.firefox
flatpak run org.mozilla.firefox --versionSee install Firefox on Debian for firefox-esr, Mozilla APT, and Snap comparisons.
sudo flatpak install -y flathub com.valvesoftware.Steam
flatpak run com.valvesoftware.SteamSteam via Flatpak is covered in install Steam on Debian.
Launch and inspect apps
flatpak run com.github.tchx84.Flatseal
flatpak info com.github.tchx84.Flatseal | head -12Flatseal - Manage Flatpak permissions
ID: com.github.tchx84.Flatseal
Ref: app/com.github.tchx84.Flatseal/x86_64/stable
Version: 2.4.1
Origin: flathub
Installation: systemGNOME Software integration (optional)
On GNOME, install the Flatpak plugin so Software can browse Flathub:
sudo apt install -y gnome-software-plugin-flatpakKDE users can install plasma-discover-backend-flatpak when using Discover. These packages are optional—the flatpak CLI works without them.
Update Flatpak and applications
Update installed Flatpaks
flatpak updateWhen nothing is pending:
Looking for updates…
Nothing to do.Update the flatpak package itself
sudo apt update
sudo apt install --only-upgrade flatpak
flatpak --versionUninstall Flatpak applications and the framework
Remove one app
flatpak uninstall com.github.tchx84.Flatseal
flatpak uninstall --user io.github.zaedus.spiderRemove unused runtimes after deleting apps:
flatpak uninstall --unusedRemove the flatpak package
sudo apt purge flatpak
sudo apt autoremove --purgeDry-run removing flatpak:
The following packages will be REMOVED:
flatpak
Remv flatpak [1.16.6-1~deb13u1]Delete leftover data
sudo rm -rf /var/lib/flatpak
rm -rf ~/.local/share/flatpakInstalled Flatpak apps stop working if you delete these directories without uninstalling first.
Troubleshooting
| Symptom | Likely cause | Fix |
|---|---|---|
flatpak: command not found |
Package not installed | sudo apt install flatpak |
error: No remote refs found for 'flathub' (user install) |
Flathub missing at user scope | flatpak remote-add --user … flathub.flatpakrepo |
| App missing from menu after install | Session cache | Log out/in; run update-desktop-database |
| Blank window / no file picker | Portal not installed | sudo apt install xdg-desktop-portal xdg-desktop-portal-gtk |
Very large disk use under /var/lib/flatpak |
Shared runtimes per app | flatpak uninstall --unused; remove apps you do not need |
Flatpak Firefox vs firefox-esr confusion |
Multiple channels | Pick one primary browser—see install Firefox on Debian |
| Old Flatpak on Bullseye | Stable only has older build | Enable bullseye-backports per Debian Wiki — Flatpak |
References
- Flatpak — Debian setup
- Flatpak — official setup index
- Debian Wiki — Flatpak
- Flathub
- flatpak package on Debian
- On-site: install Firefox on Debian, install Steam on Debian, list installed packages on Debian, install sudo on Debian, apt command
Summary
Install Flatpak on Debian with sudo apt install flatpak, add Flathub via flatpak remote-add, and install apps with flatpak install flathub APP_ID. Use system scope (sudo) or --user scope for per-account installs—add Flathub at the matching scope. Update apps with flatpak update, list them with flatpak list, and remove flatpak plus /var/lib/flatpak when you no longer need sandboxed packages.
