diff --git a/source/targetfiltersource.go b/source/targetfiltersource.go
index 5c95ecfda5..24d6c56e47 100644
--- a/source/targetfiltersource.go
+++ b/source/targetfiltersource.go
@@ -52,6 +52,11 @@ func (ms *targetFilterSource) Endpoints(ctx context.Context) ([]*endpoint.Endpoi
 			}
 		}
 
+		// If all targets are filtered out, skip the endpoint.
+		if len(filteredTargets) == 0 {
+			continue
+		}
+
 		ep.Targets = filteredTargets
 
 		result = append(result, ep)