diff --git a/eos-updater/apply.c b/eos-updater/apply.c
index 374d76e4..b16809ed 100644
--- a/eos-updater/apply.c
+++ b/eos-updater/apply.c
@@ -27,6 +27,7 @@
 #include <libeos-updater-util/types.h>
 #include <libeos-updater-util/util.h>
 #include <ostree.h>
+#include <libmount.h>
 
 /* Closure containing the data for the apply worker thread. The
  * worker thread must not access EosUpdater or EosUpdaterData directly,
@@ -227,6 +228,65 @@ update_remote_branches (OstreeRepo   *repo,
   return TRUE;
 }
 
+static gboolean
+sysroot_boot_is_automount (OstreeSysroot *sysroot)
+{
+  GFile *sysroot_file;
+  g_autoptr(GFile) boot_file = NULL;
+  g_autofree gchar *boot_path = NULL;
+  gboolean ret = FALSE;
+  struct libmnt_table *tb = NULL;
+  struct libmnt_cache *cache;
+  struct libmnt_fs *fs;
+
+  sysroot_file = ostree_sysroot_get_path (sysroot);
+  boot_file = g_file_get_child (sysroot_file, "boot");
+  boot_path = g_file_get_path (boot_file);
+  if (boot_path == NULL)
+    {
+      g_autofree gchar *sysroot_path = g_file_get_path (sysroot_file);
+      g_warning ("No boot directory in sysroot %s", sysroot_path);
+      goto out;
+    }
+
+  tb = mnt_new_table_from_file ("/proc/self/mountinfo");
+  if (tb == NULL)
+    {
+      g_warning ("Failed to parse /proc/self/mountinfo: %s",
+                 g_strerror (errno));
+      goto out;
+    }
+
+  cache = mnt_new_cache ();
+  if (cache == NULL)
+    {
+      g_warning ("Failed to create libmount cache: %s", g_strerror (errno));
+      goto out;
+    }
+  mnt_table_set_cache (tb, cache);
+  mnt_unref_cache (cache);
+
+  /* Find the /boot mountpoint iterating forward so that the autofs mount is
+   * found and not the automount target filesystem.
+   */
+  fs = mnt_table_find_mountpoint (tb, boot_path, MNT_ITER_FORWARD);
+  if (fs == NULL)
+    {
+      g_warning ("Failed to find mountpoint for %s", boot_path);
+      goto out;
+    }
+
+  ret = g_strcmp0 (mnt_fs_get_fstype (fs), "autofs") == 0;
+  g_debug ("Boot directory %s is%s on an autofs filesystem",
+           boot_path, ret ? "" : " not");
+
+ out:
+  if (tb != NULL)
+    mnt_unref_table (tb);
+
+  return ret;
+}
+
 static gboolean
 apply_internal (ApplyData     *apply_data,
                 GCancellable  *cancellable,
@@ -270,11 +330,13 @@ apply_internal (ApplyData     *apply_data,
 
   origin = ostree_sysroot_origin_new_from_refspec (sysroot, update_refspec);
 
-  /* When booted into an OSTree system, stage the deployment so that the
-   * /etc merge happens during shutdown. Otherwise (primarily the test
-   * suite), deploy the finalized tree immediately.
+  /* When booted into an OSTree system without an automount /boot, stage the
+   * deployment so that the /etc merge happens during shutdown. Otherwise
+   * (primarily sd-boot and the test suite), deploy the finalized tree
+   * immediately.
    */
-  staged_deploy = ostree_sysroot_is_booted (sysroot);
+  staged_deploy = ostree_sysroot_is_booted (sysroot) &&
+    !sysroot_boot_is_automount (sysroot);
   if (staged_deploy)
     {
       g_message ("Creating staged deployment for revision %s", update_id);
diff --git a/eos-updater/meson.build b/eos-updater/meson.build
index 61156308..e522e3cf 100644
--- a/eos-updater/meson.build
+++ b/eos-updater/meson.build
@@ -73,7 +73,10 @@ eos_updater_sources = [
   'poll-common.h',
 ] + eos_updater_resources
 
-eos_updater_deps = libeos_updater_dbus_deps + [libeos_updater_dbus_dep]
+eos_updater_deps = libeos_updater_dbus_deps + [
+  dependency('mount', version: '>= 2.24'),
+  libeos_updater_dbus_dep,
+]
 
 eos_updater_cppflags = [
   '-DG_LOG_DOMAIN="eos-updater"',