diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index e53f6e0af..689827227 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -44,6 +44,7 @@ import (
 	promlogflag "github.com/prometheus/common/promlog/flag"
 	"github.com/prometheus/prometheus/config"
 	"github.com/prometheus/prometheus/discovery"
+	sd_config "github.com/prometheus/prometheus/discovery/config"
 	"github.com/prometheus/prometheus/notifier"
 	"github.com/prometheus/prometheus/promql"
 	"github.com/prometheus/prometheus/retrieval"
@@ -234,11 +235,12 @@ func main() {
 		ctxWeb, cancelWeb = context.WithCancel(context.Background())
 		ctxRule           = context.Background()
 
-		notifier         = notifier.New(&cfg.notifier, log.With(logger, "component", "notifier"))
-		discoveryManager = discovery.NewManager(log.With(logger, "component", "discovery manager"))
-		scrapeManager    = retrieval.NewScrapeManager(log.With(logger, "component", "scrape manager"), fanoutStorage)
-		queryEngine      = promql.NewEngine(fanoutStorage, &cfg.queryEngine)
-		ruleManager      = rules.NewManager(&rules.ManagerOptions{
+		notifier               = notifier.New(&cfg.notifier, log.With(logger, "component", "notifier"))
+		discoveryManagerScrape = discovery.NewManager(log.With(logger, "component", "discovery manager scrape"))
+		discoveryManagerNotify = discovery.NewManager(log.With(logger, "component", "discovery manager notify"))
+		scrapeManager          = retrieval.NewScrapeManager(log.With(logger, "component", "scrape manager"), fanoutStorage)
+		queryEngine            = promql.NewEngine(fanoutStorage, &cfg.queryEngine)
+		ruleManager            = rules.NewManager(&rules.ManagerOptions{
 			Appendable:  fanoutStorage,
 			QueryFunc:   rules.EngineQueryFunc(queryEngine),
 			NotifyFunc:  sendAlerts(notifier, cfg.web.ExternalURL.String()),
@@ -283,7 +285,21 @@ func main() {
 		remoteStorage.ApplyConfig,
 		webHandler.ApplyConfig,
 		notifier.ApplyConfig,
-		discoveryManager.ApplyConfig,
+		func(cfg *config.Config) error {
+			c := make(map[string]sd_config.ServiceDiscoveryConfig)
+			for _, v := range cfg.ScrapeConfigs {
+				c[v.JobName] = v.ServiceDiscoveryConfig
+			}
+			return discoveryManagerScrape.ApplyConfig(c)
+		},
+		func(cfg *config.Config) error {
+			c := make(map[string]sd_config.ServiceDiscoveryConfig)
+			for _, v := range cfg.AlertingConfig.AlertmanagerConfigs {
+				// AlertmanagerConfigs doesn't hold an unique identifier so we use the config pointer as the identifier.
+				c[fmt.Sprintf("%p", v)] = v.ServiceDiscoveryConfig
+			}
+			return discoveryManagerNotify.ApplyConfig(c)
+		},
 		scrapeManager.ApplyConfig,
 		func(cfg *config.Config) error {
 			// Get all rule files matching the configuration oaths.
@@ -332,23 +348,37 @@ func main() {
 		)
 	}
 	{
-		ctxDiscovery, cancelDiscovery := context.WithCancel(context.Background())
+		ctx, cancel := context.WithCancel(context.Background())
 		g.Add(
 			func() error {
-				err := discoveryManager.Run(ctxDiscovery)
-				level.Info(logger).Log("msg", "Discovery manager stopped")
+				err := discoveryManagerScrape.Run(ctx)
+				level.Info(logger).Log("msg", "Scrape discovery manager stopped")
 				return err
 			},
 			func(err error) {
-				level.Info(logger).Log("msg", "Stopping discovery manager...")
-				cancelDiscovery()
+				level.Info(logger).Log("msg", "Stopping scrape discovery manager...")
+				cancel()
+			},
+		)
+	}
+	{
+		ctx, cancel := context.WithCancel(context.Background())
+		g.Add(
+			func() error {
+				err := discoveryManagerNotify.Run(ctx)
+				level.Info(logger).Log("msg", "Notify discovery manager stopped")
+				return err
+			},
+			func(err error) {
+				level.Info(logger).Log("msg", "Stopping notify discovery manager...")
+				cancel()
 			},
 		)
 	}
 	{
 		g.Add(
 			func() error {
-				err := scrapeManager.Run(discoveryManager.SyncCh())
+				err := scrapeManager.Run(discoveryManagerScrape.SyncCh())
 				level.Info(logger).Log("msg", "Scrape manager stopped")
 				return err
 			},
@@ -493,7 +523,7 @@ func main() {
 		// so keep this interrupt after the ruleManager.Stop().
 		g.Add(
 			func() error {
-				notifier.Run()
+				notifier.Run(discoveryManagerNotify.SyncCh())
 				return nil
 			},
 			func(err error) {
diff --git a/discovery/manager.go b/discovery/manager.go
index 0ce6b9fc5..5372a7870 100644
--- a/discovery/manager.go
+++ b/discovery/manager.go
@@ -20,7 +20,6 @@ import (
 	"github.com/go-kit/kit/log"
 	"github.com/go-kit/kit/log/level"
 
-	"github.com/prometheus/prometheus/config"
 	sd_config "github.com/prometheus/prometheus/discovery/config"
 	"github.com/prometheus/prometheus/discovery/targetgroup"
 
@@ -101,13 +100,13 @@ func (m *Manager) SyncCh() <-chan map[string][]*targetgroup.Group {
 }
 
 // ApplyConfig removes all running discovery providers and starts new ones using the provided config.
-func (m *Manager) ApplyConfig(cfg *config.Config) error {
+func (m *Manager) ApplyConfig(cfg map[string]sd_config.ServiceDiscoveryConfig) error {
 	err := make(chan error)
 	m.actionCh <- func(ctx context.Context) {
 		m.cancelDiscoverers()
-		for _, scfg := range cfg.ScrapeConfigs {
-			for provName, prov := range m.providersFromConfig(scfg.ServiceDiscoveryConfig) {
-				m.startProvider(ctx, poolKey{setName: scfg.JobName, provider: provName}, prov)
+		for name, scfg := range cfg {
+			for provName, prov := range m.providersFromConfig(scfg) {
+				m.startProvider(ctx, poolKey{setName: name, provider: provName}, prov)
 			}
 		}
 		close(err)
diff --git a/notifier/notifier.go b/notifier/notifier.go
index dfd858f43..bd4229a22 100644
--- a/notifier/notifier.go
+++ b/notifier/notifier.go
@@ -113,9 +113,8 @@ type Notifier struct {
 	ctx    context.Context
 	cancel func()
 
-	alertmanagers   []*alertmanagerSet
-	cancelDiscovery func()
-	logger          log.Logger
+	alertmanagers map[string]*alertmanagerSet
+	logger        log.Logger
 }
 
 // Options are the configurable parameters of a Handler.
@@ -247,7 +246,7 @@ func (n *Notifier) ApplyConfig(conf *config.Config) error {
 	n.opts.ExternalLabels = conf.GlobalConfig.ExternalLabels
 	n.opts.RelabelConfigs = conf.AlertingConfig.AlertRelabelConfigs
 
-	amSets := []*alertmanagerSet{}
+	amSets := make(map[string]*alertmanagerSet)
 
 	for _, cfg := range conf.AlertingConfig.AlertmanagerConfigs {
 		ams, err := newAlertmanagerSet(cfg, n.logger)
@@ -257,7 +256,8 @@ func (n *Notifier) ApplyConfig(conf *config.Config) error {
 
 		ams.metrics = n.metrics
 
-		amSets = append(amSets, ams)
+		// The config pointer is used for the map lookup identifier.
+		amSets[fmt.Sprintf("%p", cfg)] = ams
 	}
 
 	n.alertmanagers = amSets
@@ -292,11 +292,14 @@ func (n *Notifier) nextBatch() []*Alert {
 }
 
 // Run dispatches notifications continuously.
-func (n *Notifier) Run() {
+func (n *Notifier) Run(tsets <-chan map[string][]*targetgroup.Group) {
+
 	for {
 		select {
 		case <-n.ctx.Done():
 			return
+		case ts := <-tsets:
+			n.reload(ts)
 		case <-n.more:
 		}
 		alerts := n.nextBatch()
@@ -311,6 +314,20 @@ func (n *Notifier) Run() {
 	}
 }
 
+func (n *Notifier) reload(tgs map[string][]*targetgroup.Group) {
+	n.mtx.Lock()
+	defer n.mtx.Unlock()
+
+	for id, tgroup := range tgs {
+		am, ok := n.alertmanagers[id]
+		if !ok {
+			level.Error(n.logger).Log("msg", "couldn't sync alert manager set", "err", fmt.Sprintf("invalid id:%v", id))
+			continue
+		}
+		am.sync(tgroup)
+	}
+}
+
 // Send queues the given notification requests for processing.
 // Panics if called on a handler that is not running.
 func (n *Notifier) Send(alerts ...*Alert) {
@@ -515,9 +532,9 @@ func newAlertmanagerSet(cfg *config.AlertmanagerConfig, logger log.Logger) (*ale
 	return s, nil
 }
 
-// Sync extracts a deduplicated set of Alertmanager endpoints from a list
+// sync extracts a deduplicated set of Alertmanager endpoints from a list
 // of target groups definitions.
-func (s *alertmanagerSet) Sync(tgs []*targetgroup.Group) {
+func (s *alertmanagerSet) sync(tgs []*targetgroup.Group) {
 	all := []alertmanager{}
 
 	for _, tg := range tgs {
diff --git a/retrieval/manager.go b/retrieval/manager.go
index 5cf05b79b..4f2f77c82 100644
--- a/retrieval/manager.go
+++ b/retrieval/manager.go
@@ -62,9 +62,7 @@ func (m *ScrapeManager) Run(tsets <-chan map[string][]*targetgroup.Group) error
 		case f := <-m.actionCh:
 			f()
 		case ts := <-tsets:
-			if err := m.reload(ts); err != nil {
-				level.Error(m.logger).Log("msg", "error reloading the scrape manager", "err", err)
-			}
+			m.reload(ts)
 		case <-m.graceShut:
 			return nil
 		}
@@ -129,11 +127,12 @@ func (m *ScrapeManager) Targets() []*Target {
 	return <-targets
 }
 
-func (m *ScrapeManager) reload(t map[string][]*targetgroup.Group) error {
+func (m *ScrapeManager) reload(t map[string][]*targetgroup.Group) {
 	for tsetName, tgroup := range t {
 		scrapeConfig, ok := m.scrapeConfigs[tsetName]
 		if !ok {
-			return fmt.Errorf("target set '%v' doesn't have valid config", tsetName)
+			level.Error(m.logger).Log("msg", "error reloading target set", "err", fmt.Sprintf("invalid config id:%v", tsetName))
+			continue
 		}
 
 		// Scrape pool doesn't exist so start a new one.
@@ -155,6 +154,4 @@ func (m *ScrapeManager) reload(t map[string][]*targetgroup.Group) error {
 			delete(m.scrapePools, name)
 		}
 	}
-
-	return nil
 }