diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index 1043bd3df..30e8869d3 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -155,6 +155,7 @@ func Main() int {
 	prometheus.MustRegister(configSuccess)
 	prometheus.MustRegister(configSuccessTime)
 
+	go ruleManager.Run()
 	defer ruleManager.Stop()
 
 	go notificationHandler.Run()
diff --git a/rules/manager.go b/rules/manager.go
index 3592e76fb..84eb0697e 100644
--- a/rules/manager.go
+++ b/rules/manager.go
@@ -325,6 +325,7 @@ type Manager struct {
 	opts   *ManagerOptions
 	groups map[string]*Group
 	mtx    sync.RWMutex
+	block  chan struct{}
 }
 
 // ManagerOptions bundles options for the Manager.
@@ -341,10 +342,16 @@ func NewManager(o *ManagerOptions) *Manager {
 	manager := &Manager{
 		groups: map[string]*Group{},
 		opts:   o,
+		block:  make(chan struct{}),
 	}
 	return manager
 }
 
+// Run starts processing of the rule manager.
+func (m *Manager) Run() {
+	close(m.block)
+}
+
 // Stop the rule manager's rule evaluation cycles.
 func (m *Manager) Stop() {
 	log.Info("Stopping rule manager...")
@@ -398,7 +405,13 @@ func (m *Manager) ApplyConfig(conf *config.Config) bool {
 				oldg.stop()
 				newg.copyState(oldg)
 			}
-			go newg.run()
+			go func() {
+				// Wait with starting evaluation until the rule manager
+				// is told to run. This is necessary to avoid running
+				// queries against a bootstrapping storage.
+				<-m.block
+				newg.run()
+			}()
 			wg.Done()
 		}(newg)
 	}
diff --git a/web/ui/bindata.go b/web/ui/bindata.go
index 92ccc2bd5..2c968cb04 100644
--- a/web/ui/bindata.go
+++ b/web/ui/bindata.go
@@ -134,7 +134,7 @@ func webUiTemplatesAlertsHtml() (*asset, error) {
 		return nil, err
 	}
 
-	info := bindataFileInfo{name: "web/ui/templates/alerts.html", size: 1704, mode: os.FileMode(420), modTime: time.Unix(1450348695, 0)}
+	info := bindataFileInfo{name: "web/ui/templates/alerts.html", size: 1704, mode: os.FileMode(420), modTime: time.Unix(1450878652, 0)}
 	a := &asset{bytes: bytes, info: info}
 	return a, nil
 }