diff --git a/src/libostree/ostree-repo-checkout.c b/src/libostree/ostree-repo-checkout.c
index f506545529..60ced404a0 100644
--- a/src/libostree/ostree-repo-checkout.c
+++ b/src/libostree/ostree-repo-checkout.c
@@ -1036,6 +1036,16 @@ checkout_tree_at_recurse (OstreeRepo *self, OstreeRepoCheckoutAtOptions *options
       contents_csum_v = NULL; /* iter_loop freed it */
     }
 
+  /* In this mode, we're flattening in a manner similar to overlayfs, so ensure
+   * any content that was there before is gone.
+   */
+  if (!is_opaque_whiteout && options->process_whiteouts
+      && options->overwrite_mode == OSTREE_REPO_CHECKOUT_OVERWRITE_UNION_FILES)
+    {
+      if (!glnx_shutil_rm_rf_at (destination_parent_fd, destination_name, NULL, error))
+        return FALSE;
+    }
+
   /* First, make the directory.  Push a new scope in case we end up using
    * setfscreatecon().
    */
diff --git a/tests/basic-test.sh b/tests/basic-test.sh
index 7905e6ee68..af7c2e0d28 100644
--- a/tests/basic-test.sh
+++ b/tests/basic-test.sh
@@ -1159,6 +1159,14 @@ if touch overlay/baz/.wh.cow && touch overlay/.wh.deeper && touch overlay/baz/an
     assert_has_file overlay-co/baz
     test -L overlay-co/anewdir
 
+    rm overlay-co overlay -rf
+    mkdir -p overlay/somelink
+    $OSTREE --repo=repo commit ${COMMIT_ARGS} -b overlay-symlink-convert --tree=dir=overlay
+    for branch in test2 overlay-symlink-convert; do
+        $OSTREE --repo=repo checkout --union --whiteouts ${branch} overlay-co
+    done
+    test -d overlay-co/somelink || fatal "should replace symlink with dir"
+    rm overlay-co overlay -rf
     echo "ok whiteouts enabled"
 
     # Now double check whiteouts are not processed without --whiteouts