Preheat oven to 350 degrees F (175 degrees C).

Line a deep baking dish with aluminum foil.

Rinse and drain quinoa.

Combine quinoa and water in a saucepan.

Bring to a boil.

Cover, reduce heat, and simmer for 15 minutes, or until quinoa is tender and water is absorbed.

Heat olive oil in a large skillet over medium heat.

Add diced onion and minced garlic to the skillet.

Cook, stirring occasionally, until fragrant and slightly translucent, about 5-7 minutes.

Add diced zucchini, eggplant, and tomato to the skillet.

Cook until slightly tender, about 3-5 minutes.

Stir in tomato sauce.

Cover and simmer for 10 more minutes, or until vegetables have softened.

Stir cooked quinoa into the vegetable mixture.

Season with salt and pepper to taste.

Cut tops off bell peppers and remove seeds.

Fill each bell pepper with the quinoa-vegetable mixture.

Place stuffed peppers in the prepared baking dish.

Cover the dish with aluminum foil.

Bake in the preheated oven for 18 minutes, or until bell peppers are slightly tender.

Remove aluminum foil cover.

Sprinkle the tops of the peppers with shredded mozzarella cheese.

Bake until cheese is bubbling and melted, about 5 more minutes.

Serve hot.