Cook quinoa according to package instructions.
In a large skillet, over medium heat, heat 2 tablespoons of olive oil. Add the mushrooms and onion, and cook, stirring, until softened and all the moisture has disappeared (about 10 minutes).
Add the garlic and cook for 30 seconds. Stir in the canned tomatoes, thyme, salt, and black pepper. Simmer over low heat for about 10 minutes more.
Turn off the heat and stir in the cooked quinoa, Parmesan cheese, almonds, and parsley.
Preheat the oven to 400°F (200°C).
Place the pepper halves, cut sides up, in a large baking dish. Spoon the mushroom quinoa mixture into the peppers, mounding if necessary. Drizzle with the remaining tablespoon olive oil and lemon juice.
Cover with foil and bake for about 50 minutes - 1 hour, or until the peppers reach your desired level of tenderness.
Uncover, top with the shredded mozzarella cheese, and bake for 5-10 minutes more until the cheese has melted.