diff --git a/infra-tools/internal/renderdiff/engine.go b/infra-tools/internal/renderdiff/engine.go
index 8d569bfd462..359a3c86044 100644
--- a/infra-tools/internal/renderdiff/engine.go
+++ b/infra-tools/internal/renderdiff/engine.go
@@ -159,8 +159,13 @@ func (e *Engine) buildPair(cd *ComponentDiff) error {
 		cd.BaseYAML = baseYAML
 	}
 
-	// If neither side has the directory, nothing to diff.
+	// If neither side produced output, check whether the directory exists.
+	// Empty-base overlays (resources: []) intentionally produce no output;
+	// treat them as a no-op instead of an error.
 	if cd.HeadYAML == nil && cd.BaseYAML == nil {
+		if e.head.DirExists(cd.Path) || e.base.DirExists(cd.Path) {
+			return nil
+		}
 		return fmt.Errorf("component %s does not exist on either ref", cd.Path)
 	}
 
diff --git a/infra-tools/internal/renderdiff/engine_test.go b/infra-tools/internal/renderdiff/engine_test.go
index b37992539f8..b5b4b1ad2c8 100644
--- a/infra-tools/internal/renderdiff/engine_test.go
+++ b/infra-tools/internal/renderdiff/engine_test.go
@@ -226,6 +226,30 @@ func TestEngine_NoEffectiveChange(t *testing.T) {
 	g.Expect(result.Diffs).To(BeEmpty()) // identical YAML → omitted
 }
 
+func TestEngine_EmptyBase_NewComponent(t *testing.T) {
+	g := NewWithT(t)
+
+	// Simulates an empty-base overlay (resources: []) that produces no output.
+	// The directory exists on HEAD but not on base, and BuildKustomization
+	// returns nil (empty kustomize output). This should be silently skipped.
+	head := &fakeBuilder{
+		exist: map[string]bool{"components/foo/staging/empty-base": true},
+		yamls: map[string][]byte{"components/foo/staging/empty-base": nil},
+	}
+	base := &fakeBuilder{
+		exist: map[string]bool{},
+	}
+
+	engine := NewEngine(head, base, 2)
+	affected := map[detector.Environment][]appset.ComponentPath{
+		detector.Staging: {{Path: "components/foo/staging/empty-base"}},
+	}
+
+	result, err := engine.Run(context.Background(), affected)
+	g.Expect(err).NotTo(HaveOccurred())
+	g.Expect(result.Diffs).To(BeEmpty(), "empty-base with no output should be silently skipped")
+}
+
 func TestEngine_EmptyInput(t *testing.T) {
 	g := NewWithT(t)