diff --git a/files/usr/bin/system-flatpak-setup b/files/usr/bin/system-flatpak-setup
index 5a935a7..94de0f5 100755
--- a/files/usr/bin/system-flatpak-setup
+++ b/files/usr/bin/system-flatpak-setup
@@ -17,6 +17,14 @@ if grep -qz 'fedora' <<< $(flatpak remotes); then
   /usr/bin/fedora-third-party disable
   flatpak remote-delete fedora --force
   flatpak remote-delete fedora-testing --force
+
+  # Remove flatpak apps from origin fedora
+  FEDORA_FLATPAKS=$(flatpak list --app --columns=application,origin | grep -w 'fedora' | awk '{print $1}')
+  flatpak remove --system --noninteractive ${FEDORA_FLATPAKS[@]}
+
+  # Remove flatpak runtimes from origin fedora
+  FEDORA_FLATPAKS=$(flatpak list --runtime --columns=application,arch,branch,origin | grep -w 'fedora' | awk '{print $1"/"$2"/"$3}')
+  flatpak remove --system --noninteractive ${FEDORA_FLATPAKS[@]}
 fi
 
 REPO_INFO="/etc/flatpak/system/repo-info.yml"