diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index e1321b93a..045ec5377 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -391,7 +391,6 @@ func main() {
 		webHandler.ApplyConfig,
 		// The Scrape and notifier managers need to reload before the Discovery manager as
 		// they need to read the most updated config when receiving the new targets list.
-		notifierManager.ApplyConfig,
 		scrapeManager.ApplyConfig,
 		func(cfg *config.Config) error {
 			c := make(map[string]sd_config.ServiceDiscoveryConfig)
@@ -400,6 +399,7 @@ func main() {
 			}
 			return discoveryManagerScrape.ApplyConfig(c)
 		},
+		notifierManager.ApplyConfig,
 		func(cfg *config.Config) error {
 			c := make(map[string]sd_config.ServiceDiscoveryConfig)
 			for _, v := range cfg.AlertingConfig.AlertmanagerConfigs {