diff --git a/Atomic/syscontainers.py b/Atomic/syscontainers.py
index b11f6a1b..9d7520c2 100644
--- a/Atomic/syscontainers.py
+++ b/Atomic/syscontainers.py
@@ -401,12 +401,11 @@ def uninstall_system_container(self, name):
         except subprocess.CalledProcessError:
             pass
 
+        if os.path.lexists("%s/%s" % (self._get_system_checkout_path(), name)):
+            os.unlink("%s/%s" % (self._get_system_checkout_path(), name))
         for deploy in ["0", "1"]:
             if os.path.exists("%s/%s.%s" % (self._get_system_checkout_path(), name, deploy)):
                 shutil.rmtree("%s/%s.%s" % (self._get_system_checkout_path(), name, deploy))
-        if os.path.exists("%s/%s" % (self._get_system_checkout_path(), name)):
-            os.unlink("%s/%s" % (self._get_system_checkout_path(), name))
-
         if os.path.exists(os.path.join(SYSTEMD_UNIT_FILES_DEST, "%s.service" % name)):
             os.unlink(os.path.join(SYSTEMD_UNIT_FILES_DEST, "%s.service" % name))
 
diff --git a/tests/integration/test_system_containers.sh b/tests/integration/test_system_containers.sh
index cf113d28..46081c75 100755
--- a/tests/integration/test_system_containers.sh
+++ b/tests/integration/test_system_containers.sh
@@ -104,6 +104,9 @@ ${ATOMIC} umount ${WORK_DIR}/mount
 
 ${ATOMIC} uninstall ${NAME}
 test \! -e /etc/systemd/system/${NAME}.service
+test \! -e ${ATOMIC_OSTREE_CHECKOUT_PATH}/${NAME}
+test \! -e ${ATOMIC_OSTREE_CHECKOUT_PATH}/${NAME}.0
+test \! -e ${ATOMIC_OSTREE_CHECKOUT_PATH}/${NAME}.1
 
 # check that there are not any "ociimage/" prefixed branch left after images prune
 ostree --repo=${ATOMIC_OSTREE_REPO} refs --delete "ociimage/atomic-test-system-latest"