diff --git a/discovery/legacymanager/manager.go b/discovery/legacymanager/manager.go
index 87823f401..e7c79a8f8 100644
--- a/discovery/legacymanager/manager.go
+++ b/discovery/legacymanager/manager.go
@@ -270,7 +270,12 @@ func (m *Manager) updateGroup(poolKey poolKey, tgs []*targetgroup.Group) {
 	}
 	for _, tg := range tgs {
 		if tg != nil { // Some Discoverers send nil target group so need to check for it to avoid panics.
-			m.targets[poolKey][tg.Source] = tg
+			// Remove the deleted target.
+			if len(tg.Targets) == 0 && len(tg.Labels) == 0 {
+				delete(m.targets[poolKey], tg.Source)
+			} else {
+				m.targets[poolKey][tg.Source] = tg
+			}
 		}
 	}
 }
diff --git a/discovery/legacymanager/manager_test.go b/discovery/legacymanager/manager_test.go
index 13b84e6e3..bc8a419ec 100644
--- a/discovery/legacymanager/manager_test.go
+++ b/discovery/legacymanager/manager_test.go
@@ -824,13 +824,9 @@ func TestTargetSetRecreatesEmptyStaticConfigs(t *testing.T) {
 	if !ok {
 		t.Fatalf("'%v' should be present in target groups", pkey)
 	}
-	group, ok := targetGroups[""]
-	if !ok {
-		t.Fatalf("missing '' key in target groups %v", targetGroups)
-	}
-
-	if len(group.Targets) != 0 {
-		t.Fatalf("Invalid number of targets: expected 0, got %d", len(group.Targets))
+	_, ok = targetGroups[""]
+	if ok {
+		t.Fatalf("Target groups should be empty, got %v", targetGroups)
 	}
 }
 
diff --git a/discovery/manager.go b/discovery/manager.go
index 8b304a0fa..7f06b423d 100644
--- a/discovery/manager.go
+++ b/discovery/manager.go
@@ -387,7 +387,12 @@ func (m *Manager) updateGroup(poolKey poolKey, tgs []*targetgroup.Group) {
 	}
 	for _, tg := range tgs {
 		if tg != nil { // Some Discoverers send nil target group so need to check for it to avoid panics.
-			m.targets[poolKey][tg.Source] = tg
+			// Remove the deleted target.
+			if len(tg.Targets) == 0 && len(tg.Labels) == 0 {
+				delete(m.targets[poolKey], tg.Source)
+			} else {
+				m.targets[poolKey][tg.Source] = tg
+			}
 		}
 	}
 }
diff --git a/discovery/manager_test.go b/discovery/manager_test.go
index 537160811..67ccbcac7 100644
--- a/discovery/manager_test.go
+++ b/discovery/manager_test.go
@@ -1044,19 +1044,8 @@ func TestTargetSetRecreatesEmptyStaticConfigs(t *testing.T) {
 	if !ok {
 		t.Fatalf("'%v' should be present in target groups", p)
 	}
-	group, ok := targetGroups[""]
-	if !ok {
-		t.Fatalf("missing '' key in target groups %v", targetGroups)
-	}
-
-	if len(group.Targets) != 0 {
-		t.Fatalf("Invalid number of targets: expected 0, got %d", len(group.Targets))
-	}
-	require.Equal(t, 1, len(syncedTargets))
-	require.Equal(t, 1, len(syncedTargets["prometheus"]))
-	if lbls := syncedTargets["prometheus"][0].Labels; lbls != nil {
-		t.Fatalf("Unexpected Group: expected nil Labels, got %v", lbls)
-	}
+	require.Equal(t, 0, len(targetGroups))
+	require.Equal(t, 0, len(syncedTargets))
 }
 
 func TestIdenticalConfigurationsAreCoalesced(t *testing.T) {