diff --git a/src/libostree/ostree-sysroot-deploy.c b/src/libostree/ostree-sysroot-deploy.c
index d026690b7b..984dec5363 100644
--- a/src/libostree/ostree-sysroot-deploy.c
+++ b/src/libostree/ostree-sysroot-deploy.c
@@ -2260,7 +2260,10 @@ swap_bootloader (OstreeSysroot *sysroot, OstreeBootloader *bootloader, int curre
    *    for whatever reason, and we wouldn't want to confuse the
    *    admin by going back to the previous session.
    */
-  if (fsync (sysroot->boot_fd) != 0)
+  glnx_autofd int boot_dir_fd = -1;
+  if (!glnx_opendirat (sysroot->boot_fd, ".", TRUE, &boot_dir_fd, error))
+    return FALSE;
+  if (fsync (boot_dir_fd) != 0)
     return glnx_throw_errno_prefix (error, "fsync(boot)");
 
   /* TODO: In the future also execute this automatically via a systemd unit