Line a baking sheet with foil. Remove the stems from the mushrooms, arrange mushrooms on the baking sheet.
Mix cream cheese, oregano, garlic and red pepper flakes until combined.
Spoon about ½ tsp of marinara sauce into each mushroom. Fill each mushroom with the cream cheese mixture, then top with the grated mozzarella.
Bake for about 15 minutes, until cheese it melted. Remove from oven and top each mushroom with 2-3 pepperoni. Return to oven and bake about 5 more minutes, until cheese is bubbly and mushrooms are tender.