diff --git a/pkg/apply/destroyer.go b/pkg/apply/destroyer.go
index 5793a07..6bd4f65 100644
--- a/pkg/apply/destroyer.go
+++ b/pkg/apply/destroyer.go
@@ -70,6 +70,11 @@ func (d *Destroyer) Run() <-chan event.Event {
 	go func() {
 		defer close(ch)
 		infos, _ := d.ApplyOptions.GetObjects()
+		// Clear the data/inventory section of the grouping object configmap,
+		// so the prune will calculate the prune set as all the objects,
+		// deleting everything. We can ignore the error, since the Prune
+		// will catch the same problems.
+		_ = prune.ClearGroupingObj(infos)
 		err := d.PruneOptions.Prune(infos, ch)
 		if err != nil {
 			// If we see an error here we just report it on the channel and then
diff --git a/pkg/apply/prune/grouping.go b/pkg/apply/prune/grouping.go
index e240d56..5e47d10 100644
--- a/pkg/apply/prune/grouping.go
+++ b/pkg/apply/prune/grouping.go
@@ -224,6 +224,39 @@ func RetrieveInventoryFromGroupingObj(infos []*resource.Info) ([]*ObjMetadata, e
 	return inventory, nil
 }
 
+// ClearGroupingObj finds the grouping object in the list of objects,
+// and sets an empty inventory. Returns error if the grouping object
+// is not Unstructured, the grouping object does not exist, or if
+// we can't set the empty inventory on the grouping object. If successful,
+// returns nil.
+func ClearGroupingObj(infos []*resource.Info) error {
+	// Initially, find the grouping object ConfigMap (in Unstructured format).
+	var groupingObj *unstructured.Unstructured
+	for _, info := range infos {
+		obj := info.Object
+		if IsGroupingObject(obj) {
+			var ok bool
+			groupingObj, ok = obj.(*unstructured.Unstructured)
+			if !ok {
+				return fmt.Errorf("grouping object is not an Unstructured: %#v", groupingObj)
+			}
+			break
+		}
+	}
+	if groupingObj == nil {
+		return fmt.Errorf("grouping object not found")
+	}
+	// Clears the inventory map of the ConfigMap "data" section.
+	emptyMap := map[string]string{}
+	err := unstructured.SetNestedStringMap(groupingObj.UnstructuredContent(),
+		emptyMap, "data")
+	if err != nil {
+		return err
+	}
+
+	return nil
+}
+
 // calcInventoryHash returns an unsigned int32 representing the hash
 // of the inventory strings. If there is an error writing bytes to
 // the hash, then the error is returned; nil is returned otherwise.
diff --git a/pkg/apply/prune/grouping_test.go b/pkg/apply/prune/grouping_test.go
index 1af749c..819cd3f 100644
--- a/pkg/apply/prune/grouping_test.go
+++ b/pkg/apply/prune/grouping_test.go
@@ -581,6 +581,65 @@ func TestAddSuffixToName(t *testing.T) {
 	}
 }
 
+func TestClearGroupingObject(t *testing.T) {
+	tests := map[string]struct {
+		infos   []*resource.Info
+		isError bool
+	}{
+		"Empty infos should error": {
+			infos:   []*resource.Info{},
+			isError: true,
+		},
+		"Non-Unstructured grouping object should error": {
+			infos:   []*resource.Info{nonUnstructuredGroupingInfo},
+			isError: true,
+		},
+		"Info with nil Object should error": {
+			infos:   []*resource.Info{nilInfo},
+			isError: true,
+		},
+		"Single grouping object should work": {
+			infos:   []*resource.Info{copyGroupingInfo()},
+			isError: false,
+		},
+		"Single non-grouping object should error": {
+			infos:   []*resource.Info{pod1Info},
+			isError: true,
+		},
+		"Multiple non-grouping objects should error": {
+			infos:   []*resource.Info{pod1Info, pod2Info},
+			isError: true,
+		},
+		"Grouping object with single inventory object should work": {
+			infos:   []*resource.Info{copyGroupingInfo(), pod1Info},
+			isError: false,
+		},
+	}
+
+	for name, tc := range tests {
+		t.Run(name, func(t *testing.T) {
+			err := ClearGroupingObj(tc.infos)
+			if tc.isError {
+				if err == nil {
+					t.Errorf("Should have produced an error, but returned none.")
+				}
+			}
+			if !tc.isError {
+				if err != nil {
+					t.Fatalf("Received unexpected error: %#v", err)
+				}
+				objMetadata, err := RetrieveInventoryFromGroupingObj(tc.infos)
+				if err != nil {
+					t.Fatalf("Received unexpected error: %#v", err)
+				}
+				if len(objMetadata) > 0 {
+					t.Errorf("Grouping object inventory not cleared: %#v\n", objMetadata)
+				}
+			}
+		})
+	}
+}
+
 func TestPrependGroupingObject(t *testing.T) {
 	tests := []struct {
 		infos []*resource.Info