diff --git a/src/libostree/ostree-repo-checkout.c b/src/libostree/ostree-repo-checkout.c
index a3dd68878c..1c923d3e0f 100644
--- a/src/libostree/ostree-repo-checkout.c
+++ b/src/libostree/ostree-repo-checkout.c
@@ -374,7 +374,8 @@ hardlink_add_tmp_name (OstreeRepo              *self,
 
 static gboolean
 checkout_file_hardlink (OstreeRepo                          *self,
-                        OstreeRepoCheckoutAtOptions           *options,
+                        const char                          *checksum,
+                        OstreeRepoCheckoutAtOptions         *options,
                         const char                          *loose_path,
                         int                                  destination_dfd,
                         const char                          *destination_name,
@@ -436,10 +437,25 @@ checkout_file_hardlink (OstreeRepo                          *self,
             if (!glnx_fstatat (destination_dfd, destination_name, &dest_stbuf,
                                AT_SYMLINK_NOFOLLOW, error))
               return FALSE;
-            const gboolean is_identical =
+            gboolean is_identical =
               (src_stbuf.st_dev == dest_stbuf.st_dev &&
                src_stbuf.st_ino == dest_stbuf.st_ino);
+            if (!is_identical && (src_stbuf.st_size == dest_stbuf.st_size))
+              {
+                /* resort to a checksum check */
+                g_autofree char *abspath =
+                  glnx_fdrel_abspath (destination_dfd, destination_name);
+                g_autoptr(GFile) dest_file = g_file_new_for_path (abspath);
+
+                /* XXX: need an fd-relative version of this API */
+                g_autofree guchar *csum = NULL;
+                if (!ostree_checksum_file (dest_file, OSTREE_OBJECT_TYPE_FILE,
+                                           &csum, cancellable, error))
+                  return FALSE;
 
+                g_autofree char *actual_checksum = ostree_checksum_from_bytes (csum);
+                is_identical = g_str_equal (checksum, actual_checksum);
+              }
             if (is_identical)
               ret_result = HARDLINK_RESULT_SKIP_EXISTED;
             else if (options->overwrite_mode == OSTREE_REPO_CHECKOUT_OVERWRITE_UNION_FILES)
@@ -563,6 +579,7 @@ checkout_one_file_at (OstreeRepo                        *repo,
                  the cache, which is in "bare" form */
               _ostree_loose_path (loose_path_buf, checksum, OSTREE_OBJECT_TYPE_FILE, OSTREE_REPO_MODE_BARE);
               if (!checkout_file_hardlink (current_repo,
+                                           checksum,
                                            options,
                                            loose_path_buf,
                                            destination_dfd, destination_name,
@@ -652,7 +669,7 @@ checkout_one_file_at (OstreeRepo                        *repo,
       }
       g_mutex_unlock (&repo->cache_lock);
 
-      if (!checkout_file_hardlink (repo, options, loose_path_buf,
+      if (!checkout_file_hardlink (repo, checksum, options, loose_path_buf,
                                    destination_dfd, destination_name,
                                    FALSE, &hardlink_res,
                                    cancellable, error))
diff --git a/tests/basic-test.sh b/tests/basic-test.sh
index 037f7b45f5..9d969b85b7 100644
--- a/tests/basic-test.sh
+++ b/tests/basic-test.sh
@@ -511,6 +511,12 @@ for x in $(seq 3); do
         assert_file_has_content union-identical-test/usr/share/licenses/${v} GPL
     done
 done
+# now checkout the first pkg in force copy mode to make sure we can checksum
+rm union-identical-test -rf
+$OSTREE checkout --force-copy union-identical-pkg${x} union-identical-test
+for x in 2 3; do
+    $OSTREE checkout ${CHECKOUT_H_ARGS} --union-identical union-identical-pkg${x} union-identical-test
+done
 echo "ok checkout union identical merges"
 
 # Make conflicting packages, one with regfile, one with symlink