diff --git a/src/ostree/ot-admin-builtin-deploy.c b/src/ostree/ot-admin-builtin-deploy.c
index 8da9dbc3..68d17e95 100644
--- a/src/ostree/ot-admin-builtin-deploy.c
+++ b/src/ostree/ot-admin-builtin-deploy.c
@@ -162,7 +162,7 @@ ot_admin_builtin_deploy (int argc, char **argv, OstreeCommandInvocation *invocat
                                    kargs_strv, &new_deployment, cancellable, error))
     return FALSE;
 
-  OstreeSysrootSimpleWriteDeploymentFlags flags = 0;
+  OstreeSysrootSimpleWriteDeploymentFlags flags = OSTREE_SYSROOT_SIMPLE_WRITE_DEPLOYMENT_FLAGS_NO_CLEAN;
   if (opt_retain)
     flags |= OSTREE_SYSROOT_SIMPLE_WRITE_DEPLOYMENT_FLAGS_RETAIN;
   else
@@ -180,5 +180,10 @@ ot_admin_builtin_deploy (int argc, char **argv, OstreeCommandInvocation *invocat
                                                merge_deployment, flags, cancellable, error))
     return FALSE;
 
+  /* And finally, cleanup of any leftover data.
+   */
+  if (!ostree_sysroot_cleanup (self, cancellable, error))
+    return FALSE;
+
   return TRUE;
 }