diff --git a/discovery/manager.go b/discovery/manager.go
index 0a3d107a3..d3cab05c4 100644
--- a/discovery/manager.go
+++ b/discovery/manager.go
@@ -73,7 +73,7 @@ func NewManager(logger log.Logger) *Manager {
 		logger:         logger,
 		actionCh:       make(chan func(context.Context)),
 		syncCh:         make(chan map[string][]*targetgroup.Group),
-		targets:        make(map[poolKey][]*targetgroup.Group),
+		targets:        make(map[poolKey]map[string]*targetgroup.Group),
 		discoverCancel: []context.CancelFunc{},
 	}
 }
@@ -83,7 +83,8 @@ type Manager struct {
 	logger         log.Logger
 	actionCh       chan func(context.Context)
 	discoverCancel []context.CancelFunc
-	targets        map[poolKey][]*targetgroup.Group
+	// We use map[string]*targetgroup.Group to handle Discoverers that send only updates instead of all targets on every update.
+	targets map[poolKey]map[string]*targetgroup.Group
 	// The sync channels sends the updates in map[targetSetName] where targetSetName is the job value from the scrape config.
 	syncCh chan map[string][]*targetgroup.Group
 }
@@ -143,8 +144,8 @@ func (m *Manager) runProvider(ctx context.Context, poolKey poolKey, updates chan
 			if !ok {
 				return
 			}
-			m.addGroup(poolKey, tgs)
-			m.syncCh <- m.allGroups(poolKey)
+			m.updateGroup(poolKey, tgs)
+			m.syncCh <- m.allGroups()
 		}
 	}
 }
@@ -153,16 +154,21 @@ func (m *Manager) cancelDiscoverers() {
 	for _, c := range m.discoverCancel {
 		c()
 	}
-	m.targets = make(map[poolKey][]*targetgroup.Group)
+	m.targets = make(map[poolKey]map[string]*targetgroup.Group)
 	m.discoverCancel = nil
 }
 
-func (m *Manager) addGroup(poolKey poolKey, tg []*targetgroup.Group) {
+func (m *Manager) updateGroup(poolKey poolKey, tg []*targetgroup.Group) {
 	done := make(chan struct{})
 
 	m.actionCh <- func(ctx context.Context) {
 		if tg != nil {
-			m.targets[poolKey] = tg
+			for _, t := range tg {
+				if _, ok := m.targets[poolKey]; !ok {
+					m.targets[poolKey] = make(map[string]*targetgroup.Group)
+				}
+				m.targets[poolKey][t.Source] = t
+			}
 		}
 		close(done)
 
@@ -170,7 +176,7 @@ func (m *Manager) addGroup(poolKey poolKey, tg []*targetgroup.Group) {
 	<-done
 }
 
-func (m *Manager) allGroups(pk poolKey) map[string][]*targetgroup.Group {
+func (m *Manager) allGroups() map[string][]*targetgroup.Group {
 	tSets := make(chan map[string][]*targetgroup.Group)
 
 	m.actionCh <- func(ctx context.Context) {
@@ -185,7 +191,9 @@ func (m *Manager) allGroups(pk poolKey) map[string][]*targetgroup.Group {
 		tSetsAll := map[string][]*targetgroup.Group{}
 		for _, pk := range pKeys {
 			for _, tg := range m.targets[pk] {
-				if tg.Source != "" { // Don't add empty targets.
+				// Don't add empty targets.
+				// Some Discoverers(eg. k8s) send only the updates so removed targets will be updated with an empty Source value.
+				if tg.Source != "" {
 					tSetsAll[pk.setName] = append(tSetsAll[pk.setName], tg)
 				}
 			}