diff --git a/internal/xds/cache/snapshotcache.go b/internal/xds/cache/snapshotcache.go
index 61b923f22c..6c989b37e4 100644
--- a/internal/xds/cache/snapshotcache.go
+++ b/internal/xds/cache/snapshotcache.go
@@ -90,7 +90,13 @@ func (s *snapshotCache) GenerateNewSnapshot(irKey string, resources types.XdsRes
 	}
 	xdsSnapshotCreateTotal.WithSuccess().Increment()
 
-	s.lastSnapshot[irKey] = snapshot
+	// Delete snapshot from cache if resources are nil
+	if resources == nil {
+		delete(s.lastSnapshot, irKey)
+	} else {
+		// Update snapshot in cache
+		s.lastSnapshot[irKey] = snapshot
+	}
 
 	for _, node := range s.getNodeIDs(irKey) {
 		s.log.Debugf("Generating a snapshot with Node %s", node)
diff --git a/internal/xds/runner/runner_test.go b/internal/xds/runner/runner_test.go
index 154edbdb8c..bb666ead0f 100644
--- a/internal/xds/runner/runner_test.go
+++ b/internal/xds/runner/runner_test.go
@@ -318,7 +318,7 @@ func TestRunner(t *testing.T) {
 	xdsIR.Delete("test")
 	require.Eventually(t, func() bool {
 		// Wait for the IR to be empty after deletion
-		return len(xdsIR.LoadAll()) == 0
+		return !r.cache.SnapshotHasIrKey("test") && len(xdsIR.LoadAll()) == 0
 	}, time.Second*5, time.Millisecond*50)
 }