Preheat oven to 400°F. Remove stems from mushrooms. Trim and finely chop stems. Place mushrooms caps on foil-lined baking pan. Set aside.
Place chorizo in large skillet on medium heat. Cook and stir until crumbled and lightly browned. Add onion; cook and stir 2 minutes or until tender. Add chopped mushroom stems, thyme and pepper; cook and stir 1 minute. Remove from heat. Stir in queso fresco. Fill each mushroom cap with about 1 tablespoon chorizo mixture.
Bake 20 minutes or until mushroom caps are tender.