diff --git a/api/v1alpha1/condition_types.go b/api/v1alpha1/condition_types.go
index a3fb88f..f1a89a4 100644
--- a/api/v1alpha1/condition_types.go
+++ b/api/v1alpha1/condition_types.go
@@ -60,6 +60,9 @@ const (
 	// ApplyFailedReason represents the fact that the kustomization apply failed.
 	ApplyFailedReason string = "ApplyFailed"
 
+	// PruneFailedReason represents the fact that the kustomization pruning failed.
+	PruneFailedReason string = "PruneFailed"
+
 	// ArtifactFailedReason represents the fact that the artifact download failed.
 	ArtifactFailedReason string = "ArtifactFailed"
 
diff --git a/api/v1alpha1/kustomization_types.go b/api/v1alpha1/kustomization_types.go
index d059d28..8103ba9 100644
--- a/api/v1alpha1/kustomization_types.go
+++ b/api/v1alpha1/kustomization_types.go
@@ -163,6 +163,20 @@ func KustomizationNotReady(kustomization Kustomization, reason, message string)
 	return kustomization
 }
 
+func KustomizationNotReadySnapshot(kustomization Kustomization, snapshot *Snapshot, reason, message string) Kustomization {
+	kustomization.Status.Conditions = []Condition{
+		{
+			Type:               ReadyCondition,
+			Status:             corev1.ConditionFalse,
+			LastTransitionTime: metav1.Now(),
+			Reason:             reason,
+			Message:            message,
+		},
+	}
+	kustomization.Status.Snapshot = snapshot
+	return kustomization
+}
+
 // GetTimeout returns the timeout with default
 func (in *Kustomization) GetTimeout() time.Duration {
 	duration := in.Spec.Interval.Duration
diff --git a/controllers/kustomization_controller.go b/controllers/kustomization_controller.go
index 1a41472..21f248f 100644
--- a/controllers/kustomization_controller.go
+++ b/controllers/kustomization_controller.go
@@ -248,11 +248,22 @@ func (r *KustomizationReconciler) sync(
 		), err
 	}
 
-	// health assessment
-	err = r.checkHealth(kustomization)
+	// prune
+	err = r.prune(kustomization, snapshot)
 	if err != nil {
 		return kustomizev1.KustomizationNotReady(
 			kustomization,
+			kustomizev1.PruneFailedReason,
+			err.Error(),
+		), err
+	}
+
+	// health assessment
+	err = r.checkHealth(kustomization)
+	if err != nil {
+		return kustomizev1.KustomizationNotReadySnapshot(
+			kustomization,
+			snapshot,
 			kustomizev1.HealthCheckFailedReason,
 			"health check failed",
 		), err
@@ -364,7 +375,7 @@ func (r *KustomizationReconciler) generateLabelTransformer(kustomization kustomi
 		}{
 			Name: kustomization.GetName(),
 		},
-		Labels: gcLabels(kustomization.GetName(), revision),
+		Labels: gcLabels(kustomization.GetName(), kustomization.GetNamespace(), revision),
 		FieldSpecs: []kustypes.FieldSpec{
 			{Path: "metadata/labels", CreateIfNotPresent: true},
 		},
@@ -476,6 +487,25 @@ func (r *KustomizationReconciler) apply(kustomization kustomizev1.Kustomization,
 	return nil
 }
 
+func (r *KustomizationReconciler) prune(kustomization kustomizev1.Kustomization, snapshot *kustomizev1.Snapshot) error {
+	if kustomization.Status.Snapshot == nil || snapshot == nil {
+		return nil
+	}
+	if kustomization.Status.Snapshot.Revision == snapshot.Revision {
+		return nil
+	}
+
+	if !prune(kustomization.GetTimeout(),
+		kustomization.GetName(),
+		kustomization.GetNamespace(),
+		kustomization.Status.Snapshot,
+		r.Log,
+	) {
+		return fmt.Errorf("pruning failed")
+	}
+	return nil
+}
+
 func (r *KustomizationReconciler) checkHealth(kustomization kustomizev1.Kustomization) error {
 	timeout := kustomization.GetTimeout() + (time.Second * 1)
 	ctx, cancel := context.WithTimeout(context.Background(), timeout)
diff --git a/controllers/kustomization_predicate.go b/controllers/kustomization_predicate.go
index 33fc34f..fad15e3 100644
--- a/controllers/kustomization_predicate.go
+++ b/controllers/kustomization_predicate.go
@@ -68,41 +68,62 @@ type KustomizationGarbageCollectPredicate struct {
 func (gc KustomizationGarbageCollectPredicate) Delete(e event.DeleteEvent) bool {
 	if k, ok := e.Object.(*kustomizev1.Kustomization); ok {
 		if k.Spec.Prune != "" && !k.Spec.Suspend && k.Status.Snapshot != nil {
-			timeout := k.GetTimeout()
-			selector := gcSelectors(k.GetName(), k.Status.Snapshot.Revision)
 			gc.Log.Info("Garbage collection started",
 				"kustomization", fmt.Sprintf("%s/%s", k.GetNamespace(), k.GetName()))
 
-			for ns, kinds := range k.Status.Snapshot.NamespacedKinds() {
-				for _, kind := range kinds {
-					if output, err := deleteByKind(timeout, kind, ns, selector); err != nil {
-						gc.Log.Error(err, "Garbage collection failed for namespaced objects",
-							"kustomization", fmt.Sprintf("%s/%s", k.GetNamespace(), k.GetName()))
-					} else {
-						gc.Log.Info("Garbage collection for namespaced objects completed",
-							"kustomization", fmt.Sprintf("%s/%s", k.GetNamespace(), k.GetName()),
-							"output", output)
-					}
-				}
-			}
-
-			for _, kind := range k.Status.Snapshot.NonNamespacedKinds() {
-				if output, err := deleteByKind(timeout, kind, "", selector); err != nil {
-					gc.Log.Error(err, "Garbage collection failed for non-namespaced objects",
-						"kustomization", fmt.Sprintf("%s/%s", k.GetNamespace(), k.GetName()))
-				} else {
-					gc.Log.Info("Garbage collection for non-namespaced objects completed",
-						"kustomization", fmt.Sprintf("%s/%s", k.GetNamespace(), k.GetName()),
-						"output", output)
-				}
-
-			}
+			prune(k.GetTimeout(), k.GetName(), k.GetNamespace(), k.Status.Snapshot, gc.Log)
 		}
 	}
 
 	return true
 }
 
+func prune(timeout time.Duration, name string, namespace string, snapshot *kustomizev1.Snapshot, log logr.Logger) bool {
+	selector := gcSelectors(name, namespace, snapshot.Revision)
+	ok := true
+	outInfo := ""
+	outErr := ""
+	for ns, kinds := range snapshot.NamespacedKinds() {
+		for _, kind := range kinds {
+			if output, err := deleteByKind(timeout, kind, ns, selector); err != nil {
+				outErr += " " + err.Error()
+				ok = false
+			} else {
+				outInfo += " " + output
+			}
+		}
+	}
+	if outErr == "" {
+		log.Info("Garbage collection for namespaced objects completed",
+			"kustomization", fmt.Sprintf("%s/%s", namespace, name),
+			"output", outInfo)
+	} else {
+		log.Error(fmt.Errorf(outErr), "Garbage collection for namespaced objects failed",
+			"kustomization", fmt.Sprintf("%s/%s", namespace, name))
+	}
+
+	outInfo = ""
+	outErr = ""
+	for _, kind := range snapshot.NonNamespacedKinds() {
+		if output, err := deleteByKind(timeout, kind, "", selector); err != nil {
+			outErr += " " + err.Error()
+			ok = false
+		} else {
+			outInfo += " " + output
+		}
+	}
+	if outErr == "" {
+		log.Info("Garbage collection for non-namespaced objects completed",
+			"kustomization", fmt.Sprintf("%s/%s", namespace, name),
+			"output", outInfo)
+	} else {
+		log.Error(fmt.Errorf(outErr), "Garbage collection for non-namespaced objects failed",
+			"kustomization", fmt.Sprintf("%s/%s", namespace, name))
+	}
+
+	return ok
+}
+
 func deleteByKind(timeout time.Duration, kind, namespace, selector string) (string, error) {
 	ctx, cancel := context.WithTimeout(context.Background(), timeout+time.Second)
 	defer cancel()
@@ -120,15 +141,15 @@ func deleteByKind(timeout time.Duration, kind, namespace, selector string) (stri
 	}
 }
 
-func gcLabels(name, revision string) map[string]string {
+func gcLabels(name, namespace, revision string) map[string]string {
 	return map[string]string{
-		"kustomization/name":     name,
+		"kustomization/name":     fmt.Sprintf("%s-%s", name, namespace),
 		"kustomization/revision": checksum(revision),
 	}
 }
 
-func gcSelectors(name, revision string) string {
-	return fmt.Sprintf("kustomization/name=%s,kustomization/revision=%s", name, checksum(revision))
+func gcSelectors(name, namespace, revision string) string {
+	return fmt.Sprintf("kustomization/name=%s-%s,kustomization/revision=%s", name, namespace, checksum(revision))
 }
 
 func checksum(in string) string {