diff --git a/discovery/manager.go b/discovery/manager.go
index bb4409fea..ab8328924 100644
--- a/discovery/manager.go
+++ b/discovery/manager.go
@@ -232,6 +232,11 @@ func (m *Manager) updateGroup(poolKey poolKey, tgs []*targetgroup.Group) {
 				m.targets[poolKey] = make(map[string]*targetgroup.Group)
 			}
 			m.targets[poolKey][tg.Source] = tg
+
+			// Clear the key in the case where the targets is empty.
+			if tg.Targets == nil || len(tg.Targets) <= 0 {
+				delete(m.targets[poolKey], tg.Source)
+			}
 		}
 	}
 }