Preheat your oven to 375°F (190°C).
Clean the mushrooms and remove the stems. Set them aside on a baking sheet.
Heat olive oil in a pan over medium heat. Add the diced onion and garlic and sauté until fragrant, about 3 minutes.
Add the cooked quinoa to the pan with the onions and garlic. Stir in parsley, thyme, salt, and pepper. Cook for another 2 minutes until the quinoa absorbs the flavors.
Spoon the quinoa mixture into each mushroom cap, pressing gently to pack it in. Top each mushroom with cheese.
Bake for 20-25 minutes, or until the mushrooms are tender and the cheese is melted and bubbly.
Optional: For a golden-brown top, broil the mushrooms for 2 minutes at the end.
Serve warm and enjoy!