diff --git a/controllers/kustomization_controller.go b/controllers/kustomization_controller.go
index c3df0a48..d90f89c1 100644
--- a/controllers/kustomization_controller.go
+++ b/controllers/kustomization_controller.go
@@ -647,6 +647,9 @@ func (r *KustomizationReconciler) apply(ctx context.Context, manager *ssa.Resour
 		return false, nil, err
 	}
 
+	applyOpts := ssa.DefaultApplyOptions()
+	applyOpts.Force = kustomization.Spec.Force
+
 	// contains only CRDs and Namespaces
 	var stageOne []*unstructured.Unstructured
 
@@ -668,7 +671,7 @@ func (r *KustomizationReconciler) apply(ctx context.Context, manager *ssa.Resour
 
 	// validate, apply and wait for CRDs and Namespaces to register
 	if len(stageOne) > 0 {
-		changeSet, err := manager.ApplyAll(ctx, stageOne, kustomization.Spec.Force)
+		changeSet, err := manager.ApplyAll(ctx, stageOne, applyOpts)
 		if err != nil {
 			return false, nil, err
 		}
@@ -683,7 +686,10 @@ func (r *KustomizationReconciler) apply(ctx context.Context, manager *ssa.Resour
 			}
 		}
 
-		if err := manager.Wait(stageOne, 2*time.Second, kustomization.GetTimeout()); err != nil {
+		if err := manager.Wait(stageOne, ssa.WaitOptions{
+			Interval: 2 * time.Second,
+			Timeout:  kustomization.GetTimeout(),
+		}); err != nil {
 			return false, nil, err
 		}
 	}
@@ -691,7 +697,7 @@ func (r *KustomizationReconciler) apply(ctx context.Context, manager *ssa.Resour
 	// sort by kind, validate and apply all the others objects
 	sort.Sort(ssa.SortableUnstructureds(stageTwo))
 	if len(stageTwo) > 0 {
-		changeSet, err := manager.ApplyAll(ctx, stageTwo, kustomization.Spec.Force)
+		changeSet, err := manager.ApplyAll(ctx, stageTwo, applyOpts)
 		if err != nil {
 			return false, nil, fmt.Errorf("%w\n%s", err, changeSetLog.String())
 		}
@@ -757,7 +763,10 @@ func (r *KustomizationReconciler) checkHealth(ctx context.Context, manager *ssa.
 	}
 
 	// check the health with a default timeout of 30sec shorter than the reconciliation interval
-	if err := manager.WaitForSet(toCheck, time.Second, kustomization.GetTimeout()); err != nil {
+	if err := manager.WaitForSet(toCheck, ssa.WaitOptions{
+		Interval: 5 * time.Second,
+		Timeout:  kustomization.GetTimeout(),
+	}); err != nil {
 		return fmt.Errorf("Health check failed after %s, %w", time.Now().Sub(checkStart).String(), err)
 	}
 
@@ -776,12 +785,16 @@ func (r *KustomizationReconciler) prune(ctx context.Context, manager *ssa.Resour
 	}
 
 	log := logr.FromContext(ctx)
-	changeSet, err := manager.DeleteAll(ctx, objects,
-		manager.GetOwnerLabels(kustomization.Name, kustomization.Namespace),
-		map[string]string{
+
+	opts := ssa.DeleteOptions{
+		PropagationPolicy: metav1.DeletePropagationBackground,
+		Inclusions:        manager.GetOwnerLabels(kustomization.Name, kustomization.Namespace),
+		Exclusions: map[string]string{
 			fmt.Sprintf("%s/prune", kustomizev1.GroupVersion.Group): kustomizev1.DisabledValue,
 		},
-	)
+	}
+
+	changeSet, err := manager.DeleteAll(ctx, objects, opts)
 	if err != nil {
 		return false, err
 	}
@@ -817,12 +830,15 @@ func (r *KustomizationReconciler) finalize(ctx context.Context, kustomization ku
 				Group: kustomizev1.GroupVersion.Group,
 			})
 
-			changeSet, err := resourceManager.DeleteAll(ctx, objects,
-				resourceManager.GetOwnerLabels(kustomization.Name, kustomization.Namespace),
-				map[string]string{
+			opts := ssa.DeleteOptions{
+				PropagationPolicy: metav1.DeletePropagationBackground,
+				Inclusions:        resourceManager.GetOwnerLabels(kustomization.Name, kustomization.Namespace),
+				Exclusions: map[string]string{
 					fmt.Sprintf("%s/prune", kustomizev1.GroupVersion.Group): kustomizev1.DisabledValue,
 				},
-			)
+			}
+
+			changeSet, err := resourceManager.DeleteAll(ctx, objects, opts)
 			if err != nil {
 				r.event(ctx, kustomization, kustomization.Status.LastAppliedRevision, events.EventSeverityError, "pruning for deleted resource failed", nil)
 				// Return the error so we retry the failed garbage collection
diff --git a/go.mod b/go.mod
index 71ec7b90..d2eb0340 100644
--- a/go.mod
+++ b/go.mod
@@ -12,7 +12,7 @@ require (
 	github.com/fluxcd/pkg/apis/kustomize v0.2.0
 	github.com/fluxcd/pkg/apis/meta v0.10.1
 	github.com/fluxcd/pkg/runtime v0.12.2
-	github.com/fluxcd/pkg/ssa v0.2.0
+	github.com/fluxcd/pkg/ssa v0.3.1
 	github.com/fluxcd/pkg/testserver v0.1.0
 	github.com/fluxcd/pkg/untar v0.1.0
 	github.com/fluxcd/source-controller/api v0.16.0
diff --git a/go.sum b/go.sum
index c90ad437..16fc25e9 100644
--- a/go.sum
+++ b/go.sum
@@ -225,8 +225,8 @@ github.com/fluxcd/pkg/apis/meta v0.10.1/go.mod h1:yUblM2vg+X8TE3A2VvJfdhkGmg+uqB
 github.com/fluxcd/pkg/runtime v0.12.0/go.mod h1:EyaTR2TOYcjL5U//C4yH3bt2tvTgIOSXpVRbWxUn/C4=
 github.com/fluxcd/pkg/runtime v0.12.2 h1:4iOpx2j/w15kNemDOnZrF6ugJ/rhSmRu7aI+xn23+BI=
 github.com/fluxcd/pkg/runtime v0.12.2/go.mod h1:tuWdqpWPhgjQvYrSnojdZ4plyU8DRU1NDzsfOhnzl2g=
-github.com/fluxcd/pkg/ssa v0.2.0 h1:5GTBnnWJhiSIKI1TZQ20ioWjTPNkEof2V2uN0ZHUxDs=
-github.com/fluxcd/pkg/ssa v0.2.0/go.mod h1:rFhWBX9/TfNwSFR+5NHOGnpl9OsWdaQrG5CggN+74EQ=
+github.com/fluxcd/pkg/ssa v0.3.1 h1:lKjTRQmSWFEXpKJadK9Fu0GSLL8lv0k5muIcc+7hZIs=
+github.com/fluxcd/pkg/ssa v0.3.1/go.mod h1:rFhWBX9/TfNwSFR+5NHOGnpl9OsWdaQrG5CggN+74EQ=
 github.com/fluxcd/pkg/testserver v0.1.0 h1:nOYgM1HYFZNNSUFykuWDmrsxj4jQxUCvmLHWOQeqmyA=
 github.com/fluxcd/pkg/testserver v0.1.0/go.mod h1:fvt8BHhXw6c1+CLw1QFZxcQprlcXzsrL4rzXaiGM+Iw=
 github.com/fluxcd/pkg/untar v0.1.0 h1:k97V/xV5hFrAkIkVPuv5AVhyxh1ZzzAKba/lbDfGo6o=