diff --git a/lib/mu-server.cc b/lib/mu-server.cc
index 08546d2b..c472ea00 100644
--- a/lib/mu-server.cc
+++ b/lib/mu-server.cc
@@ -868,6 +868,8 @@ Server::Private::index_handler (const Parameters& params)
         Mu::Indexer::Config conf{};
         conf.cleanup    = get_bool_or(params, ":cleanup");
         conf.lazy_check = get_bool_or(params, ":lazy-check");
+	// ignore .noupdate with an empty store.
+	conf.ignore_noupdate = store().empty();
 
         indexer().stop();
 
diff --git a/mu/mu-cmd-index.cc b/mu/mu-cmd-index.cc
index 49429fe0..82f6b044 100644
--- a/mu/mu-cmd-index.cc
+++ b/mu/mu-cmd-index.cc
@@ -124,6 +124,8 @@ Mu::mu_cmd_index (Mu::Store& store, const MuConfig *opts, GError **err)
         Mu::Indexer::Config conf{};
         conf.cleanup          = !opts->nocleanup;
         conf.lazy_check       = opts->lazycheck;
+	// ignore .noupdate with an empty store.
+	conf.ignore_noupdate = store.empty();
 
         install_sig_handler ();