diff --git a/CHANGELOG.md b/CHANGELOG.md
index 841f1ddb..0069f566 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,7 +33,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
   - faster reading of installed applications (subprocess call replaced by Python call)
   
 - Flatpak
-  - settings: not displaying the installation target option when bauh is launched by the root user 
+  - settings: not displaying the installation target option when bauh is launched by the root user
+  - always considering **system** as the installation level for the root user
 
 - Web
   - the Electron builds cache directory has been moved to the environment directory `~/.local/share/bauh/web/env/electron`
diff --git a/bauh/gems/flatpak/controller.py b/bauh/gems/flatpak/controller.py
index 987541b0..d0bff64c 100644
--- a/bauh/gems/flatpak/controller.py
+++ b/bauh/gems/flatpak/controller.py
@@ -375,9 +375,11 @@ class FlatpakManager(SoftwareManager):
         return True
 
     def install(self, pkg: FlatpakApplication, root_password: str, disk_loader: DiskCacheLoader, watcher: ProcessWatcher) -> TransactionResult:
-        flatpak_config = self.configman.get_config()
-
-        install_level = flatpak_config['installation_level']
+        if not self.context.root_user:
+            flatpak_config = self.configman.get_config()
+            install_level = flatpak_config['installation_level']
+        else:
+            install_level = 'system'
 
         if install_level is not None:
             self.logger.info("Default Flaptak installation level defined: {}".format(install_level))