Preheat the oven to 375°F (190°C).
In a large skillet, heat the olive oil over medium heat. Add the minced garlic and sauté for about 1 minute until fragrant.
Add the chopped spinach and cook until wilted, about 2-3 minutes. Stir in the cooked quinoa, cherry tomatoes, oregano, salt, black pepper, and red pepper flakes. Cook for another 2-3 minutes until everything is heated through.
Remove the skillet from heat and stir in half of the mozzarella cheese and half of the Parmesan cheese until well combined.
Place the portobello mushrooms, gill side up, on a baking sheet lined with parchment paper. Spoon the quinoa mixture generously into each mushroom cap.
Top each stuffed mushroom with the remaining mozzarella and Parmesan cheese.
Bake in the preheated oven for 20-25 minutes, or until the mushrooms are tender and the cheese is bubbly and golden.
Remove from the oven and let cool for a few minutes. Garnish with fresh basil if desired before serving.