diff --git a/internal/theming/theming.go b/internal/theming/theming.go
index bc176bd..b1369b4 100644
--- a/internal/theming/theming.go
+++ b/internal/theming/theming.go
@@ -140,6 +140,52 @@ func Apply(cfg config.Config, themeID string) error {
 			return fmt.Errorf("write %s: %w", tc.DestRel, err)
 		}
 	}
-	_ = cfg // overlay update lands in Task 3
+	_ = cfg // overlay carries config state; overlay file update below
+	if err := updateOverlayActive(th.ID); err != nil {
+		return fmt.Errorf("update overlay: %w", err)
+	}
 	return nil
 }
+
+// updateOverlayActive rewrites ~/.config/archduino/overlay.yaml so that
+// theme_overrides.__active reflects the selected theme, preserving all
+// other keys via a generic map round-trip.
+func updateOverlayActive(themeID string) error {
+	home, err := os.UserHomeDir()
+	if err != nil {
+		return err
+	}
+	path := filepath.Join(home, ".config", "archduino", "overlay.yaml")
+
+	var root map[string]any
+	if data, err := os.ReadFile(path); err == nil {
+		if err := yaml.Unmarshal(data, &root); err != nil {
+			return fmt.Errorf("parse overlay: %w", err)
+		}
+	}
+	if root == nil {
+		root = map[string]any{}
+	}
+
+	if _, ok := root["version"]; !ok {
+		root["version"] = 1
+	}
+
+	var overrides map[string]any
+	if raw, ok := root["theme_overrides"]; ok {
+		if m, ok := raw.(map[string]any); ok {
+			overrides = m
+		}
+	}
+	if overrides == nil {
+		overrides = map[string]any{}
+	}
+	overrides["__active"] = themeID
+	root["theme_overrides"] = overrides
+
+	out, err := yaml.Marshal(root)
+	if err != nil {
+		return err
+	}
+	return platform.WriteUserFile(path, out, 0o644)
+}
diff --git a/internal/theming/theming_test.go b/internal/theming/theming_test.go
index e7366cf..0e5f02c 100644
--- a/internal/theming/theming_test.go
+++ b/internal/theming/theming_test.go
@@ -79,3 +79,41 @@ func TestApplyUnknownThemeErrors(t *testing.T) {
 		t.Fatal("want error on unknown theme")
 	}
 }
+
+func TestApplyUpdatesOverlayActive(t *testing.T) {
+	home := t.TempDir()
+	t.Setenv("HOME", home)
+	if err := Apply(config.Config{}, "gruvbox"); err != nil {
+		t.Fatal(err)
+	}
+	data, err := os.ReadFile(filepath.Join(home, ".config", "archduino", "overlay.yaml"))
+	if err != nil {
+		t.Fatalf("overlay missing: %v", err)
+	}
+	if !strings.Contains(string(data), "__active: gruvbox") {
+		t.Fatalf("overlay missing active theme: %s", data)
+	}
+}
+
+func TestApplyPreservesOtherOverlayKeys(t *testing.T) {
+	home := t.TempDir()
+	t.Setenv("HOME", home)
+	op := filepath.Join(home, ".config", "archduino", "overlay.yaml")
+	if err := os.MkdirAll(filepath.Dir(op), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(op, []byte("version: 1\nextra_packages:\n  - foo\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	if err := Apply(config.Config{}, "gruvbox"); err != nil {
+		t.Fatal(err)
+	}
+	data, _ := os.ReadFile(op)
+	if !strings.Contains(string(data), "- foo") {
+		t.Fatalf("extra_packages lost: %s", data)
+	}
+	if !strings.Contains(string(data), "__active: gruvbox") {
+		t.Fatalf("active theme missing after preserve: %s", data)
+	}
+}