Preheat the oven to 375°F (190°C) and lightly grease a baking dish.
Slice the zucchini in half lengthwise and scoop out the centers, leaving a small border. Chop the scooped zucchini flesh and set aside.
Heat olive oil in a skillet over medium heat. Add the onion and garlic, and sauté for 2–3 minutes until fragrant.
Add the chopped zucchini flesh, bell pepper, and mushrooms. Cook for 4–5 minutes until softened.
Stir in the cooked quinoa, tomatoes, nutritional yeast, Italian seasoning, salt, and pepper. Mix well and remove from heat.
Arrange the zucchini boats in the baking dish and spoon the filling evenly into each one.
Sprinkle with dairy-free cheese if using. Cover loosely with foil and bake for 25 minutes.
Remove the foil and bake for another 10 minutes until tender. Garnish with fresh herbs and serve warm.