diff --git a/pkg/storage/unified/resource/datastore.go b/pkg/storage/unified/resource/datastore.go
index a3301062048..f939f18f1df 100644
--- a/pkg/storage/unified/resource/datastore.go
+++ b/pkg/storage/unified/resource/datastore.go
@@ -106,6 +106,7 @@ type ListRequestKey struct {
 	Group     string
 	Resource  string
 	Name      string
+	Sort      SortOrder
 }
 
 func (k ListRequestKey) Validate() error {
@@ -194,6 +195,7 @@ func (d *dataStore) Keys(ctx context.Context, key ListRequestKey) iter.Seq2[Data
 		for k, err := range d.kv.Keys(ctx, dataSection, ListOptions{
 			StartKey: prefix,
 			EndKey:   PrefixRangeEnd(prefix),
+			Sort:     key.Sort,
 		}) {
 			if err != nil {
 				yield(DataKey{}, err)
diff --git a/pkg/storage/unified/resource/storage_backend.go b/pkg/storage/unified/resource/storage_backend.go
index 0408a758b0b..4f5490f7c7d 100644
--- a/pkg/storage/unified/resource/storage_backend.go
+++ b/pkg/storage/unified/resource/storage_backend.go
@@ -85,25 +85,33 @@ func (k *kvStorageBackend) pruneEvents(ctx context.Context, key PruningKey) erro
 		return fmt.Errorf("invalid pruning key, all fields must be set: %+v", key)
 	}
 
-	keepEvents := make([]DataKey, 0, prunerMaxEvents)
-
+	listKey := ListRequestKey{
+		Namespace: key.Namespace,
+		Group:     key.Group,
+		Resource:  key.Resource,
+		Name:      key.Name,
+		Sort:      SortOrderDesc,
+	}
+	counter := 0
 	// iterate over all keys for the resource and delete versions beyond the latest 20
-	for datakey, err := range k.dataStore.Keys(ctx, ListRequestKey(key)) {
+	for datakey, err := range k.dataStore.Keys(ctx, listKey) {
 		if err != nil {
 			return err
 		}
 
-		if len(keepEvents) < prunerMaxEvents {
-			keepEvents = append(keepEvents, datakey)
+		// Pruner needs to exclude deleted events
+		if counter < prunerMaxEvents && datakey.Action != DataActionDeleted {
+			counter++
 			continue
 		}
 
-		// If we already have 20 versions, delete the oldest one and append the new one
-		err := k.dataStore.Delete(ctx, keepEvents[0])
-		if err != nil {
-			return err
+		// If we already have 20 versions, delete any more create or update events
+		if datakey.Action != DataActionDeleted {
+			err := k.dataStore.Delete(ctx, datakey)
+			if err != nil {
+				return err
+			}
 		}
-		keepEvents = append(keepEvents[1:], datakey)
 	}
 
 	return nil
diff --git a/pkg/storage/unified/resource/storage_backend_test.go b/pkg/storage/unified/resource/storage_backend_test.go
index f69a7900cc6..65cd65354d3 100644
--- a/pkg/storage/unified/resource/storage_backend_test.go
+++ b/pkg/storage/unified/resource/storage_backend_test.go
@@ -1258,6 +1258,7 @@ func TestKvStorageBackend_PruneEvents(t *testing.T) {
 			Group:     "apps",
 			Resource:  "resources",
 			Name:      "test-resource",
+			Sort:      SortOrderDesc,
 		}) {
 			require.NoError(t, err)
 			require.NotEqual(t, rv1, datakey.ResourceVersion)
@@ -1324,12 +1325,81 @@ func TestKvStorageBackend_PruneEvents(t *testing.T) {
 			Group:     "apps",
 			Resource:  "resources",
 			Name:      "test-resource",
+			Sort:      SortOrderDesc,
 		}) {
 			require.NoError(t, err)
 			counter++
 		}
 		require.Equal(t, prunerMaxEvents, counter)
 	})
+
+	t.Run("will not prune deleted events", func(t *testing.T) {
+		backend := setupTestStorageBackend(t)
+		ctx := context.Background()
+
+		// Create a resource
+		ns := NamespacedResource{
+			Namespace: "default",
+			Group:     "apps",
+			Resource:  "resources",
+		}
+		testObj, err := createTestObjectWithName("test-resource", ns, "test-data")
+		require.NoError(t, err)
+		metaAccessor, err := utils.MetaAccessor(testObj)
+		require.NoError(t, err)
+		writeEvent := WriteEvent{
+			Type: resourcepb.WatchEvent_DELETED,
+			Key: &resourcepb.ResourceKey{
+				Namespace: "default",
+				Group:     "apps",
+				Resource:  "resources",
+				Name:      "test-resource",
+			},
+			Value:      objectToJSONBytes(t, testObj),
+			Object:     metaAccessor,
+			ObjectOld:  metaAccessor,
+			PreviousRV: 0,
+		}
+		rv1, err := backend.WriteEvent(ctx, writeEvent)
+		require.NoError(t, err)
+
+		// Add prunerMaxEvents+1 deleted events
+		// Multiple deleted events for a resource shouldn't happen - this is just to ensure the pruner won't remove deleted events
+		previousRV := rv1
+		for i := 0; i < prunerMaxEvents; i++ {
+			testObj.Object["spec"].(map[string]any)["value"] = fmt.Sprintf("delete-%d", i)
+			writeEvent.Type = resourcepb.WatchEvent_DELETED
+			writeEvent.Value = objectToJSONBytes(t, testObj)
+			writeEvent.PreviousRV = previousRV
+			newRv, err := backend.WriteEvent(ctx, writeEvent)
+			require.NoError(t, err)
+			previousRV = newRv
+		}
+
+		pruningKey := PruningKey{
+			Namespace: "default",
+			Group:     "apps",
+			Resource:  "resources",
+			Name:      "test-resource",
+		}
+
+		err = backend.pruneEvents(ctx, pruningKey)
+		require.NoError(t, err)
+
+		// assert all deleted events exist
+		counter := 0
+		for _, err := range backend.dataStore.Keys(ctx, ListRequestKey{
+			Namespace: "default",
+			Group:     "apps",
+			Resource:  "resources",
+			Name:      "test-resource",
+			Sort:      SortOrderDesc,
+		}) {
+			require.NoError(t, err)
+			counter++
+		}
+		require.Equal(t, prunerMaxEvents+1, counter)
+	})
 }
 
 // createTestObject creates a test unstructured object with standard values