Fix Flatpak Apps Not Respecting GTK Themes in Ubuntu 24.04

If a Flatpak app opens with Adwaita while the rest of Ubuntu 24.04 uses Yaru, the theme files installed on your desktop may be fine. Flatpak runs apps in a sandbox, so a program does not automatically read every host theme file. The fix is usually to make sure the selected theme is available to the Flatpak runtime and that the desktop settings service can communicate the active choice.

This guide starts with simple checks and moves to targeted troubleshooting. It applies primarily to GTK 3 applications. GTK 4 and libadwaita apps may follow different styling rules, so a theme that works in Files or another GTK 3 app is not guaranteed to apply to every Flatpak window.

What you need to know first

A GTK theme controls the appearance of interface elements such as buttons and menus in apps using GTK, a toolkit for building graphical interfaces. A Flatpak runtime provides shared libraries used by a sandboxed app. The sandbox keeps the app’s filesystem separate from the host system. As a result, host theme files under locations such as /usr/share/themes are not simply copied into every Flatpak.

Flatpak’s supported approach for GTK 3 themes is an extension named for the theme, commonly following org.gtk.Gtk3theme.ThemeName. If that extension exists in the configured remote for the app’s runtime, Flatpak can install it along with the app or during an update. The desktop must also expose the active setting: XSettings is used on X11, while the Settings portal supplies it on Wayland. A portal is a desktop service that gives sandboxed apps controlled access to selected desktop functions and preferences.

Ubuntu’s default Yaru theme is installed on the host, but that fact alone does not prove a corresponding Flatpak theme extension is available for every app and runtime. Availability can depend on the theme name, configured Flatpak remote, runtime branch, and toolkit. Flatpak documents Adwaita as the fallback when a theme or settings interface is unavailable.

Step 1: Confirm the host theme and session

First check whether the theme is applied to ordinary desktop apps. Open Settings → Appearance, note the selected style, and open a preinstalled GTK app. If host apps also look wrong, fix the desktop appearance before changing Flatpak settings.

You can inspect the GTK theme name from Terminal with:

gsettings get org.gnome.desktop.interface gtk-theme

The result is a quoted name, for example 'Yaru'. Record the spelling and capitalization. Flatpak matches the host’s selected GTK theme name to an extension; searching for a similar but differently named theme may not solve the mismatch. Ubuntu’s Yaru project documents Yaru as Ubuntu’s default GTK theme suite.

Also identify whether your session is Wayland or X11. On the login screen, select your user and use the gear menu if available; the session name is usually shown there. This matters because the settings path differs: Wayland relies on a portal, while X11 uses XSettings. Ubuntu 24.04’s default GNOME session commonly uses Wayland, but users can choose another session.

Step 2: Update Flatpak and check theme extension availability

Run a general Flatpak update so installed apps, runtimes, and available extensions can be refreshed:

flatpak update

Review the proposed changes before confirming. Next, search the configured remotes for extensions matching the theme name you recorded. For a Yaru selection, try:

flatpak search org.gtk.Gtk3theme.Yaru

If the search returns a matching extension, note the exact application ID and remote shown. Install it only if Flatpak has not already installed it. Use the ID and remote exactly as displayed:

flatpak install REMOTE EXTENSION_ID

Replace both capitalized placeholders with the actual values. Do not copy a guessed extension ID from an unrelated theme or runtime branch. Some extension builds may be unavailable for a given runtime; in that case, the app can continue to use Adwaita even though the host has Yaru.

Flatpak’s own desktop integration documentation says matching GTK theme extensions are automatically installed during app installation or update when they are present in the remote. Therefore, if the extension is available but absent, updating the app can be sufficient. Search results can vary as remotes and packages change, so treat your local Flatpak output as the current check rather than assuming a package name.

Step 3: Restart the app and refresh the desktop settings service

Close the affected app completely, including any background instance, then open it again. A running process may retain the appearance settings it read at startup.

If you use Wayland and several GTK Flatpaks still ignore the selected style, check whether the GTK portal backend is installed:

dpkg -l xdg-desktop-portal xdg-desktop-portal-gtk

Look for an installed status in the package listing. The Flatpak documentation specifically identifies xdg-desktop-portal-gtk as required for GTK themes and fonts. If it is missing, install the Ubuntu package from the official archive:

sudo apt update
sudo apt install xdg-desktop-portal-gtk

Save work in open applications first. Then sign out and sign back in, which cleanly restarts the user session and its portal services. This is usually the clearest option for a beginner. Advanced users can restart their user services from Terminal with systemctl --user restart xdg-desktop-portal.service xdg-desktop-portal-gtk.service, but service names and activation behavior can differ by installation. If that command reports that a unit is not loaded, use a sign-out instead of repeatedly restarting services.

Step 4: Check whether the application supports the theme

Reopen the same Flatpak and compare its buttons, menus, and window content with a GTK app installed from Ubuntu’s packages. If only one Flatpak differs, the problem may be specific to that app’s toolkit, runtime, or implementation. For example, some GTK 4 apps use libadwaita, which intentionally follows GNOME’s design conventions and does not support arbitrary GTK themes in the same way older GTK 3 apps do. Flatpak extensions for GTK 3 will not restyle a Qt app, either.

When an app uses a recent runtime and a GTK 3 theme extension is present, the desktop setting should normally be applied automatically. If it is not, check the app’s runtime with:

flatpak info APP_ID

Replace APP_ID with the app’s actual ID. The output helps you identify the runtime and branch to report if you contact the app maintainer. It does not by itself prove whether the application honors GTK theme preferences.

Common fixes to avoid

• Do not grant broad host filesystem access as the first fix. Flatpak documentation notes that exposing host theme files can weaken the sandbox and reduce portability. Prefer a maintained theme extension and working desktop integration.
• Do not assume installing a theme with APT installs it inside every Flatpak. APT changes the host. The Flatpak runtime still needs a compatible extension or supported settings path.
• Do not confuse dark mode with a GTK theme. The desktop’s color-scheme preference and a full GTK theme are related but distinct settings. The app and its runtime must support the relevant preference.
• Do not reset all GNOME settings or delete theme folders. Such steps can remove unrelated preferences and do not add a missing Flatpak extension.
• Do not use environment-variable overrides as a universal solution. An override can vary by toolkit and app, and may conceal the actual missing extension or portal issue.

Verify the result

After updating or installing the matching extension and restarting the session or app, confirm three things: the host still reports the expected GTK theme name; the relevant theme extension appears in Flatpak’s installed applications; and the affected app’s GTK controls now follow the expected appearance. You can list installed Flatpaks with:

flatpak list --app

If the host theme is correct, the extension is unavailable for the app’s runtime, and only one application remains visually different, the limitation may be app-specific rather than a broken Ubuntu theme. Include the Flatpak app ID, runtime branch, session type, theme name, and relevant portal package status when filing a report. This gives maintainers the details needed to distinguish a packaging gap from a desktop settings problem.

Official references

• Flatpak desktop integration: themes and appearance settings
• Flatpak extensions, including GTK 3 theme extensions
• Flatpak portal support in GTK
• Ubuntu Yaru theme suite
• Ubuntu 24.04 package details for xdg-desktop-portal-gtk