diff --git a/common/flatpak-dir.c b/common/flatpak-dir.c
index eba81fef..134024e2 100644
--- a/common/flatpak-dir.c
+++ b/common/flatpak-dir.c
@@ -7532,8 +7532,13 @@ export_desktop_file (const char         *app,
       g_key_file_remove_key (keyfile, groups[i], "X-GNOME-Bugzilla-ExtraInfoScript", NULL);
 
       new_exec = g_string_new ("");
-      if ((flatpak = g_getenv ("FLATPAK_BINARY")) == NULL)
-        flatpak = FLATPAK_BINDIR "/flatpak";
+      if (g_str_has_suffix (name, ".service"))
+      {
+        flatpak = "/run/current-system/sw/bin/flatpak";
+      } else {
+        if ((flatpak = g_getenv ("FLATPAK_BINARY")) == NULL)
+          flatpak = "flatpak";
+      }
 
       g_string_append_printf (new_exec,
                               "%s run --branch=%s --arch=%s",
@@ -8867,7 +8872,7 @@ flatpak_dir_deploy (FlatpakDir          *self,
                                        error))
         return FALSE;
       if ((flatpak = g_getenv ("FLATPAK_BINARY")) == NULL)
-        flatpak = FLATPAK_BINDIR "/flatpak";
+        flatpak = "flatpak";
 
       bin_data = g_strdup_printf ("#!/bin/sh\nexec %s run --branch=%s --arch=%s %s \"$@\"\n",
                                   flatpak, escaped_branch, escaped_arch, escaped_app);