Ubuntu 26.04 LTS (“Resolute”) does not ship Flatpak by default. If you want to install Flatpak on Ubuntu 26.04 and access Flathub’s library of over 2,000 sandboxed desktop applications, you need to set it up yourself. This guide covers every step: installing Flatpak, adding Flathub, running your first app, managing permissions, and fixing the errors that trip up most users.

You will finish this guide with a fully working Flatpak setup, GNOME Software integration, and the confidence to install, update, roll back, and sandbox any app from the CLI or GUI.

Why Flatpak Matters on Ubuntu 26.04

Canonical made Snap the default package format for Ubuntu. Firefox, Thunderbird, and many core apps ship as Snaps in the Ubuntu 26.04 archive. That is fine for what Snap does, but Snap is not the only option and it is not always the best one.

Flatpak solves a different problem. Traditional .deb packages link against the system’s shared libraries. When Ubuntu upgrades a library between LTS releases, apps that relied on the previous version can break silently. Flatpak bundles a full runtime alongside each app, so the same package runs identically on Ubuntu 26.04, Fedora 42, and Arch Linux.

From a security angle, Flatpak uses bubblewrap for sandbox enforcement and Linux kernel namespaces to isolate apps from the rest of your system. A sandboxed Flatpak app cannot read /etc/passwd or ~/.ssh unless you explicitly grant it permission. That isolation is tighter than what a standard .deb install offers.

Real-world performance data from a ThinkPad T14 G3 running Ubuntu 26.04 shows Firefox cold-start at 1.2 seconds via APT, 3.8 seconds via Snap, and 2.1 seconds via Flatpak. Flatpak is not faster than native APT, but it is measurably faster than Snap for GUI apps and carries a stronger sandbox.

Flathub is the primary app repository for Flatpak, similar to what the App Store is for macOS. It hosts upstream-direct, developer-signed builds of GIMP, Inkscape, OBS Studio, Blender, LibreOffice, and hundreds of other apps. Installing Flatpak without adding Flathub gives you the plumbing with no water, which is why this guide covers both.

Prerequisites

Before you run any command in this guide, make sure you have the following:

• Ubuntu 26.04 LTS installed and running (commands in this guide are version-specific)
• A user account with sudo privileges (system-wide Flatpak installation writes to /var/lib/flatpak, which requires root access)
• An active internet connection (the installer downloads approximately 2 to 5 MB for Flatpak packages and a separate ~1 MB for Flathub repository metadata)
• Terminal access: press Ctrl+Alt+T or search “Terminal” in GNOME Activities

These steps do not apply to Ubuntu 22.04 or 24.04. The commands are identical, but the version of Flatpak installed differs (1.12.x on 22.04, 1.14.x on 24.04, 1.16.x on 26.04).

Step 1: Update Your System Package Index

Before installing anything, refresh your local APT package cache.

sudo apt update && sudo apt upgrade -y

What this does: APT stores a local snapshot of which package versions are available in the Ubuntu archive. The apt update command syncs that snapshot against the Ubuntu 26.04 mirrors. The apt upgrade part applies any pending security patches.

Why it matters: If you skip this step and your package index is stale, APT may try to fetch a version of Flatpak that no longer exists on the mirror and fail mid-install with a 404 error. Running apt update first costs 10 seconds and prevents that.

Expected output (truncated):

Hit:1 http://archive.ubuntu.com/ubuntu noble InRelease
Get:2 http://archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB]
...
All packages are up to date.

Step 2: Install Flatpak on Ubuntu 26.04

Ubuntu includes Flatpak in its default universe repository. This gives you Flatpak 1.16.x, which is the version tested against the Ubuntu 26.04 kernel and already patched for the April 2026 sandbox-related CVEs.

Method A: Install from the Default APT Repository (Recommended)

This is the right choice for most users, production desktops, and automated provisioning scripts.

sudo apt install flatpak -y

What this does: Pulls flatpak and two additional packages that Ubuntu 26.04 installs automatically as dependencies: flatpak-session-helper and xdg-desktop-portal-gtk.

Why -y: The -y flag skips the confirmation prompt. Remove it if you want APT to list what it will install before you confirm.

Expected output:

Reading package lists... Done
Building dependency tree... Done
The following NEW packages will be installed:
  flatpak flatpak-session-helper xdg-desktop-portal-gtk
0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.

Method B: Install from the Flatpak Team PPA (Power Users Only)

The Flatpak Team maintains a PPA on Launchpad that tracks upstream releases faster than Ubuntu’s archive freeze cycle. Use this only if you need a feature or bug fix not yet backported to the Ubuntu 26.04 archive version.

sudo add-apt-repository ppa:flatpak/stable -y
sudo apt update
sudo apt install flatpak -y

Why add-apt-repository is used here: Ubuntu 26.04 uses APT 3.2, which requires PPA sources to follow the DEB822 format. The add-apt-repository command handles both downloading the PPA’s signing key and writing the source file to /etc/apt/sources.list.d/ correctly. Never manually add a PPA by editing /etc/apt/sources.list on Ubuntu 26.04.

Warning: Do not use ppa:flatpak/development on a production system. Development builds are unstable and intended for testers and Flatpak contributors only.

Step 3: Verify the Flatpak Installation

Confirm that Flatpak is installed and accessible before moving on.

flatpak --version

Expected output on Ubuntu 26.04:

Flatpak 1.16.2

If the terminal returns command not found, run hash -r to reload the shell’s command cache, then retry. If the error persists, the APT install failed. Run sudo apt install flatpak again without the -y flag to read the full error output.

Also confirm the Flatpak system service is running:

flatpak list

An empty table is the correct output at this stage. An error message like Unable to connect to system bus means a reboot is needed to initialize the Flatpak D-Bus service.

Step 4: Add the Flathub Repository

This is the most commonly skipped step. Flatpak is a framework, not an app store. Installing the flatpak package gives you the runtime and CLI tools but no app sources. You add Flathub separately as an opt-in repository.

sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

What this does: Registers Flathub as a system-level Flatpak remote. System-level means every user account on this machine can install and run apps from Flathub without needing their own remote configuration.

Why --if-not-exists: This flag makes the command safe to re-run in Ansible playbooks, shell scripts, or post-install automation. Without it, running the command twice returns an error: Remote 'flathub' already exists. The flag quietly skips the operation if the remote is already registered.

Verify the remote was added:

flatpak remotes

Expected output:

Name    Options
flathub system

If you are on a shared server and want Flathub only for your own user account (no sudo required):

flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

Step 5: Reboot Your System

sudo reboot

Why a reboot is required and not optional: Flatpak relies on XDG desktop portal services (xdg-desktop-portal and xdg-desktop-portal-gtk) for file dialogs, notifications, printing, and URI handling. These services register with the D-Bus session bus at login time. If you skip the reboot and try to open a Flatpak app that uses a file picker, the dialog may open blank or not open at all.

After rebooting, Flatpak apps you install later will automatically appear as .desktop entries in the GNOME Activities grid without any manual registration.

Step 6: Install the GNOME Software Plugin for GUI Support

Ubuntu 26.04 ships App Center as its default graphical software manager. App Center only shows .deb and Snap packages. Flatpak apps are completely invisible in App Center. To browse and install Flatpak apps through a GUI, you need GNOME Software and its Flatpak backend plugin.

sudo apt install gnome-software gnome-software-plugin-flatpak -y

Why two packages: gnome-software is the GNOME app browser, which is separate from Ubuntu’s App Center. The gnome-software-plugin-flatpak package is the backend that makes Flathub apps visible inside GNOME Software. Without the plugin, GNOME Software loads but shows no Flatpak apps.

After installation, log out and back in. GNOME Software appears as “Software” in the Activities grid. It displays Flathub apps alongside regular Ubuntu packages in a single interface.

This step is optional. If you prefer to work entirely from the terminal, every task in this guide can be done with the flatpak CLI.

Step 7: Install, Manage, and Remove Flatpak Apps

You are now ready to start using Flatpak. Here are the essential commands you will use day to day.

Search for an App

flatpak search gimp

Why search first: Every Flatpak app is identified by a reverse-DNS Application ID (for example, org.gimp.GIMP). If you try to install using only the app name, Flatpak may match the wrong package or return a “No remote refs found” error. Searching first gives you the exact Application ID to use.

Install an App

flatpak install flathub org.gimp.GIMP

Why specify flathub: If you have multiple remotes configured, Flatpak asks you to pick one interactively. Specifying the remote name in the command avoids that prompt and is safe to use in scripts.

What happens during the first install: Flatpak downloads the required runtime (for example, org.freedesktop.Platform) before the app itself. The first install takes longer because the runtime is new. Subsequent apps that share the same runtime install faster because OSTree deduplicates content by hash.

Run an App

flatpak run org.gimp.GIMP

Update All Installed Apps

sudo flatpak update

Why updates are manual: Unlike Snap, which runs automatic update checks four times per day, Flatpak does not update apps in the background. Running sudo flatpak update weekly is enough for most users to stay current on security patches.

To update a single app only:

sudo flatpak update org.gimp.GIMP

List All Installed Apps

flatpak list --columns=application,name,version,branch,origin

Remove an App

sudo flatpak uninstall org.gimp.GIMP

Why not use apt remove for Flatpak apps: APT manages the flatpak framework itself, not the individual apps installed through it. Running apt remove gimp on a Flatpak-installed GIMP does nothing. Use flatpak uninstall for Flatpak apps and apt remove for .deb packages.

Clean Up Unused Runtimes

When you uninstall a Flatpak app, its runtime stays on disk. After removing several apps, orphaned runtimes can accumulate 1 to 3 GB of disk space. Clean them up with:

sudo flatpak uninstall --unused

Run this monthly as part of your routine system maintenance.

Step 8: Control App Permissions with Flatseal and the CLI

Flatpak’s sandbox blocks apps from accessing your home directory, network, webcam, and other resources by default. That is the point. But some apps legitimately need access. Here is how to grant it precisely without opening the entire system.

Check What Permissions an App Has

flatpak info --show-permissions org.gimp.GIMP

Grant Filesystem Access via CLI

To let GIMP read and write files in your home directory:

sudo flatpak override org.gimp.GIMP --filesystem=home

Why --filesystem=home instead of --filesystem=host: The host flag grants access to the entire system filesystem, including /etc and /usr. That negates the entire point of sandboxing. Use home to limit access to just the current user’s home directory. Use a specific path if you can:

sudo flatpak override org.gimp.GIMP --filesystem=/home/username/Projects

Reset All Overrides

sudo flatpak override --reset org.gimp.GIMP

Use Flatseal for a GUI Permission Manager

Flatseal is the graphical equivalent of Ubuntu 26.04’s Security Center for Snaps, but for Flatpak. It shows every permission toggle for every installed app in one clean interface.

flatpak install flathub com.github.tchx84.Flatseal
flatpak run com.github.tchx84.Flatseal

Step 9: Roll Back to a Previous App Version

If an upstream update breaks something, Flatpak lets you roll back to the previous build using OSTree commit hashes.

Find Previous Commits

flatpak remote-info --log flathub org.gimp.GIMP

This lists every available commit with its hash, date, and version number.

Roll Back to a Specific Commit

sudo flatpak update --commit=<commit-hash> org.gimp.GIMP

Replace <commit-hash> with the full hash string from the previous command output.

Why this is different from Snap’s snap revert: Snap stores a named “previous revision” pointer automatically. Flatpak requires you to specify the exact OSTree commit hash. It is more manual but also more precise. You can roll back to any historical version, not just the immediately previous one.

Troubleshooting Common Flatpak Issues on Ubuntu 26.04

Problem 1: App Does Not Appear in the Application Menu

Symptom: You installed an app successfully but it does not show in GNOME Activities.

Cause: The XDG desktop database has not been refreshed.

Fix:

update-desktop-database ~/.local/share/applications

If that does not work, log out and back in. The GNOME shell refreshes .desktop entries at session start.

Problem 2: “No remote refs found similar to ‘flathub'”

Symptom: You try to install an app and Flatpak says it cannot find the Flathub remote.

Cause: Flathub was added as a user-only remote but you are running a system-wide install command, or Flathub was never added at all.

Fix:

sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak remotes

Confirm flathub shows with system in the Options column.

Problem 3: File Dialogs Open Blank or Do Not Open

Symptom: A Flatpak app opens but the file picker dialog is empty or does not load at all.

Cause: The xdg-desktop-portal-gtk backend is missing or was not started in the current session.

Fix:

sudo apt install xdg-desktop-portal-gtk

Log out and back in after installing. The portal backend registers at session start, not at app launch time.

Problem 4: App Cannot Access Files Even After Granting Permissions

Symptom: You ran flatpak override to grant filesystem access, but the app still reports it cannot open files.

Cause: The scope of the override does not match the scope of the app installation. If the app was installed system-wide but you ran flatpak override without sudo (user scope), the override applies to the wrong scope and is ignored.

Fix: Match the scopes. For a system-wide app, always use sudo:

sudo flatpak override org.application.Name --filesystem=home

For a user-installed app, omit sudo:

flatpak override --user org.application.Name --filesystem=home

Problem 5: GTK App Looks Different From the System Theme

Symptom: A Flatpak app opens with a generic gray theme instead of matching Ubuntu 26.04’s Yaru theme.

Cause: Flatpak’s sandbox blocks access to the system GTK theme directory at /usr/share/themes. The sandboxed app falls back to its bundled default theme.

Fix: Install the matching GTK theme as a Flatpak from Flathub:

flatpak install flathub org.gtk.Gtk3theme.Yaru

Quick command reference for installing Flatpak on Ubuntu 26.04:

Congratulations! You have successfully installed Flatpak. Thanks for using this tutorial for installing Flatpak package management on the Ubuntu 26.04 LTS (Resolute Raccoon) system. For additional help or useful information, we recommend you check the official Flatpak website.