diff --git a/retrieval/target.go b/retrieval/target.go
index 7dd8cbd2d..43c19ca4e 100644
--- a/retrieval/target.go
+++ b/retrieval/target.go
@@ -167,7 +167,6 @@ type Target struct {
 	scraperStopping chan struct{}
 	// Closing scraperStopped signals that scraping has been stopped.
 	scraperStopped chan struct{}
-	running        bool
 
 	// Mutex protects the members below.
 	sync.RWMutex
@@ -388,11 +387,9 @@ func (t *Target) InstanceIdentifier() string {
 
 // RunScraper implements Target.
 func (t *Target) RunScraper(sampleAppender storage.SampleAppender) {
-	defer close(t.scraperStopped)
+	log.Debugf("Running scraper for %v", t)
 
-	t.Lock()
-	t.running = true
-	t.Unlock()
+	defer close(t.scraperStopped)
 
 	lastScrapeInterval := t.interval()
 
@@ -452,14 +449,6 @@ func (t *Target) RunScraper(sampleAppender storage.SampleAppender) {
 
 // StopScraper implements Target.
 func (t *Target) StopScraper() {
-	t.Lock()
-	if !t.running {
-		t.Unlock()
-		return
-	}
-	t.running = false
-	t.Unlock()
-
 	log.Debugf("Stopping scraper for target %v...", t)
 
 	close(t.scraperStopping)
diff --git a/retrieval/targetmanager.go b/retrieval/targetmanager.go
index ceb880b0d..6f2cd67f5 100644
--- a/retrieval/targetmanager.go
+++ b/retrieval/targetmanager.go
@@ -73,38 +73,9 @@ func (tm *TargetManager) Run() {
 	log.Info("Starting target manager...")
 
 	tm.mtx.Lock()
+
 	tm.ctx, tm.cancel = context.WithCancel(context.Background())
-
-	jobs := map[string]struct{}{}
-
-	// Start new target sets and update existing ones.
-	for _, scfg := range tm.scrapeConfigs {
-		jobs[scfg.JobName] = struct{}{}
-
-		ts, ok := tm.targetSets[scfg.JobName]
-		if !ok {
-			ts = newTargetSet(scfg, tm.appender)
-			tm.targetSets[scfg.JobName] = ts
-		}
-		ts.runProviders(tm.ctx, providersFromConfig(scfg))
-	}
-
-	// Stop old target sets.
-	for name := range tm.targetSets {
-		if _, ok := jobs[name]; !ok {
-			delete(tm.targetSets, name)
-		}
-	}
-
-	// Run target sets.
-	for _, ts := range tm.targetSets {
-		tm.wg.Add(1)
-
-		go func(ts *targetSet) {
-			ts.run(tm.ctx)
-			tm.wg.Done()
-		}(ts)
-	}
+	tm.reload()
 
 	tm.mtx.Unlock()
 
@@ -128,6 +99,38 @@ func (tm *TargetManager) Stop() {
 	log.Debugln("Target manager stopped")
 }
 
+func (tm *TargetManager) reload() {
+	jobs := map[string]struct{}{}
+
+	// Start new target sets and update existing ones.
+	for _, scfg := range tm.scrapeConfigs {
+		jobs[scfg.JobName] = struct{}{}
+
+		ts, ok := tm.targetSets[scfg.JobName]
+		if !ok {
+			ts = newTargetSet(scfg, tm.appender)
+			tm.targetSets[scfg.JobName] = ts
+
+			tm.wg.Add(1)
+
+			go func(ts *targetSet) {
+				ts.runScraping(tm.ctx)
+				tm.wg.Done()
+			}(ts)
+		}
+		ts.runProviders(tm.ctx, providersFromConfig(scfg))
+	}
+
+	// Remove old target sets. Waiting for stopping is already guaranteed
+	// by the goroutine that started the target set.
+	for name, ts := range tm.targetSets {
+		if _, ok := jobs[name]; !ok {
+			ts.cancel()
+			delete(tm.targetSets, name)
+		}
+	}
+}
+
 // Pools returns the targets currently being scraped bucketed by their job name.
 func (tm *TargetManager) Pools() map[string][]*Target {
 	tm.mtx.RLock()
@@ -151,21 +154,14 @@ func (tm *TargetManager) Pools() map[string][]*Target {
 // by the new cfg. The state of targets that are valid in the new configuration remains unchanged.
 // Returns true on success.
 func (tm *TargetManager) ApplyConfig(cfg *config.Config) bool {
-	tm.mtx.RLock()
-	running := tm.ctx != nil
-	tm.mtx.RUnlock()
-
-	if running {
-		tm.Stop()
-		defer func() {
-			go tm.Run()
-		}()
-	}
-
 	tm.mtx.Lock()
-	tm.scrapeConfigs = cfg.ScrapeConfigs
-	tm.mtx.Unlock()
+	defer tm.mtx.Unlock()
 
+	tm.scrapeConfigs = cfg.ScrapeConfigs
+
+	if tm.ctx != nil {
+		tm.reload()
+	}
 	return true
 }
 
@@ -180,8 +176,9 @@ type targetSet struct {
 	scrapePool *scrapePool
 	config     *config.ScrapeConfig
 
-	stopProviders func()
-	syncCh        chan struct{}
+	syncCh          chan struct{}
+	cancelScraping  func()
+	cancelProviders func()
 }
 
 func newTargetSet(cfg *config.ScrapeConfig, app storage.SampleAppender) *targetSet {
@@ -194,7 +191,21 @@ func newTargetSet(cfg *config.ScrapeConfig, app storage.SampleAppender) *targetS
 	return ts
 }
 
-func (ts *targetSet) run(ctx context.Context) {
+func (ts *targetSet) cancel() {
+	ts.mtx.RLock()
+	defer ts.mtx.RUnlock()
+
+	if ts.cancelScraping != nil {
+		ts.cancelScraping()
+	}
+	if ts.cancelProviders != nil {
+		ts.cancelProviders()
+	}
+}
+
+func (ts *targetSet) runScraping(ctx context.Context) {
+	ctx, ts.cancelScraping = context.WithCancel(ctx)
+
 	ts.scrapePool.ctx = ctx
 
 Loop:
@@ -234,10 +245,10 @@ func (ts *targetSet) runProviders(ctx context.Context, providers map[string]Targ
 
 	var wg sync.WaitGroup
 
-	if ts.stopProviders != nil {
-		ts.stopProviders()
+	if ts.cancelProviders != nil {
+		ts.cancelProviders()
 	}
-	ctx, ts.stopProviders = context.WithCancel(ctx)
+	ctx, ts.cancelProviders = context.WithCancel(ctx)
 
 	for name, prov := range providers {
 		wg.Add(1)
@@ -373,7 +384,7 @@ func (sp *scrapePool) sync(tgroups map[string]map[model.Fingerprint]*Target) {
 				go tnew.RunScraper(sp.appender)
 			}
 		}
-		for fp, told := range targets {
+		for fp, told := range prevTargets {
 			// A previous target is no longer in the group.
 			if _, ok := targets[fp]; !ok {
 				wg.Add(1)
@@ -388,7 +399,7 @@ func (sp *scrapePool) sync(tgroups map[string]map[model.Fingerprint]*Target) {
 
 	// Stop scrapers for target groups that disappeared completely.
 	for source, targets := range sp.tgroups {
-		if _, ok := tgroups[source]; !ok {
+		if _, ok := tgroups[source]; ok {
 			continue
 		}
 		for _, told := range targets {