Preheat the oven to 375°F (190°C).
Clean the portobello mushrooms with a damp paper towel and place them on a baking sheet, gill side up.
In a large mixing bowl, combine the cooked quinoa, chopped spinach, cherry tomatoes, mozzarella cheese, Parmesan cheese, minced garlic, olive oil, oregano, salt, black pepper, and red pepper flakes. Mix well until all ingredients are evenly combined.
Spoon the quinoa mixture generously into each portobello mushroom cap, pressing down lightly to pack the filling.
Bake in the preheated oven for 25-30 minutes, or until the mushrooms are tender and the cheese is melted and bubbly.
Remove from the oven and let cool for a few minutes. Garnish with fresh basil if desired before serving.