diff --git a/pkg/apply/prune/prune.go b/pkg/apply/prune/prune.go
index 72687056..5db251ef 100644
--- a/pkg/apply/prune/prune.go
+++ b/pkg/apply/prune/prune.go
@@ -13,6 +13,7 @@ package prune
 
 import (
 	"sort"
+	"strings"
 
 	apierrors "k8s.io/apimachinery/pkg/api/errors"
 	"k8s.io/apimachinery/pkg/api/meta"
@@ -82,8 +83,15 @@ type Options struct {
 // objects. Returns an error if there was a problem.
 func (po *PruneOptions) Prune(localInv *unstructured.Unstructured, localObjs []*unstructured.Unstructured, currentUIDs sets.String,
 	eventChannel chan<- event.Event, o Options) error {
-	invNamespace := localInv.GetNamespace()
+	invNamespace := strings.TrimSpace(strings.ToLower(localInv.GetNamespace()))
 	klog.V(4).Infof("prune local inventory object: %s/%s", invNamespace, localInv.GetName())
+	// Create the set of namespaces for currently (locally) applied objects, including
+	// the namespace the inventory object lives in (if it's not cluster-scoped). When
+	// pruning, check this set of namespaces to ensure these namespaces are not deleted.
+	localNamespaces := mergeObjNamespaces(localObjs)
+	if invNamespace != "" {
+		localNamespaces.Insert(invNamespace)
+	}
 	clusterObjs, err := po.InvClient.GetClusterObjs(localInv)
 	if err != nil {
 		return err
@@ -126,11 +134,12 @@ func (po *PruneOptions) Prune(localInv *unstructured.Unstructured, localObjs []*
 			eventChannel <- createPruneEvent(obj, event.PruneSkipped)
 			continue
 		}
-		// If regular pruning (not destroying), skip deleting inventory namespace.
+		// If regular pruning (not destroying), skip deleting namespace containing
+		// currently applied objects.
 		if !po.Destroy {
 			if clusterObj.GroupKind == object.CoreV1Namespace.GroupKind() &&
-				clusterObj.Name == invNamespace {
-				klog.V(7).Infof("skip pruning inventory namespace: %s", obj)
+				localNamespaces.Has(strings.ToLower(clusterObj.Name)) {
+				klog.V(7).Infof("skip pruning namespace: %s", clusterObj.Name)
 				eventChannel <- createPruneEvent(obj, event.PruneSkipped)
 				continue
 			}
@@ -148,6 +157,20 @@ func (po *PruneOptions) Prune(localInv *unstructured.Unstructured, localObjs []*
 	return po.InvClient.Replace(localInv, localIds)
 }
 
+// mergeObjNamespaces returns a set of strings of all the namespaces
+// for non cluster-scoped objects. These namespaces are forced to
+// lower-case.
+func mergeObjNamespaces(objs []*unstructured.Unstructured) sets.String {
+	namespaces := sets.NewString()
+	for _, obj := range objs {
+		namespace := strings.TrimSpace(strings.ToLower(obj.GetNamespace()))
+		if namespace != "" {
+			namespaces.Insert(namespace)
+		}
+	}
+	return namespaces
+}
+
 // preventDeleteAnnotation returns true if the "onRemove:keep"
 // annotation exists within the annotation map; false otherwise.
 func preventDeleteAnnotation(annotations map[string]string) bool {
diff --git a/pkg/apply/prune/prune_test.go b/pkg/apply/prune/prune_test.go
index 7863e176..fa13d7b3 100644
--- a/pkg/apply/prune/prune_test.go
+++ b/pkg/apply/prune/prune_test.go
@@ -20,7 +20,7 @@ import (
 
 var testNamespace = "test-inventory-namespace"
 var inventoryObjName = "test-inventory-obj"
-var namespaceName = "namespace"
+var podName = "pod-1"
 var pdbName = "pdb"
 var roleName = "role"
 
@@ -45,7 +45,18 @@ var namespace = &unstructured.Unstructured{
 		"apiVersion": "v1",
 		"kind":       "Namespace",
 		"metadata": map[string]interface{}{
-			"name":      namespaceName,
+			"name": testNamespace,
+			"uid":  "uid1",
+		},
+	},
+}
+
+var pod = &unstructured.Unstructured{
+	Object: map[string]interface{}{
+		"apiVersion": "v1",
+		"kind":       "Pod",
+		"metadata": map[string]interface{}{
+			"name":      podName,
 			"namespace": testNamespace,
 			"uid":       "uid1",
 		},
@@ -150,6 +161,12 @@ func TestPrune(t *testing.T) {
 			prunedObjs:  []*unstructured.Unstructured{},
 			isError:     false,
 		},
+		"Namespace not pruned if objects are still in it": {
+			pastObjs:    []*unstructured.Unstructured{namespace, pdb, pod},
+			currentObjs: []*unstructured.Unstructured{pod},
+			prunedObjs:  []*unstructured.Unstructured{pdb},
+			isError:     false,
+		},
 	}
 	for name, tc := range tests {
 		for i := range common.Strategies {