diff --git a/usr/bin/ublue-system-flatpak-manager b/usr/bin/ublue-system-flatpak-manager
index 3b8fd846706..a503caaa8ee 100755
--- a/usr/bin/ublue-system-flatpak-manager
+++ b/usr/bin/ublue-system-flatpak-manager
@@ -55,5 +55,8 @@ if grep -qz 'fedora' <<< $(flatpak remotes); then
   done
 fi
 
+# Disable the system variant of the flathub repo
+flatpak remote-modify flathub --disable --system
+
 mkdir -p /etc/ublue
 echo $VER > $VER_FILE