diff --git a/usr/bin/ublue-system-flatpak-manager b/usr/bin/ublue-system-flatpak-manager
index d4c3fca76cb..7b0ff1b3d08 100755
--- a/usr/bin/ublue-system-flatpak-manager
+++ b/usr/bin/ublue-system-flatpak-manager
@@ -48,7 +48,14 @@ if grep -qz 'fedora' <<< $(flatpak remotes); then
   /usr/bin/fedora-third-party disable
   flatpak remote-delete fedora --force
 
-  FEDORA_FLATPAKS=$(flatpak list --columns=application,origin | grep -w 'fedora' | awk '{print $1}')
+  # Remove flatpak apps from origin fedora
+  FEDORA_FLATPAKS=$(flatpak list --app --columns=application,origin | grep -w 'fedora' | awk '{print $1}')
+  for flatpak in $FEDORA_FLATPAKS; do
+    flatpak remove --system --noninteractive $flatpak
+  done
+
+  # Remove flatpak runtimes from origin fedora
+  FEDORA_FLATPAKS=$(flatpak list --runtime --columns=application,origin | grep -w 'fedora' | awk '{print $1}')
   for flatpak in $FEDORA_FLATPAKS; do
     flatpak remove --system --noninteractive $flatpak
   done