diff --git a/lib/mu-server.cc b/lib/mu-server.cc
index 13779dfc..70fa9d25 100644
--- a/lib/mu-server.cc
+++ b/lib/mu-server.cc
@@ -767,6 +767,8 @@ 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 d7788c29..61856f48 100644
--- a/mu/mu-cmd-index.cc
+++ b/mu/mu-cmd-index.cc
@@ -120,6 +120,8 @@ 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();