Heat the oven to 350°F (175°C). Line a baking sheet with foil.
Remove and discard (or save) the mushroom stems, then arrange the mushroom caps stem-side up on the prepared baking sheet.
In a mixing bowl, combine the softened cream cheese, minced garlic, dried oregano, and red pepper flakes until smooth and evenly mixed.
Spoon about 1/2 teaspoon of marinara sauce into the bottom of each mushroom cap.
Fill each mushroom with the cream cheese mixture, pressing it gently to mound slightly, then sprinkle the grated mozzarella evenly over the tops.
Bake for about 15 minutes, until the cheese is melted and mushrooms begin to soften.
Remove the baking sheet from the oven and place 2–3 mini pepperoni on each mushroom, then return to the oven and bake about 5 more minutes, until cheese is bubbly and mushrooms are tender.
Garnish with chopped parsley, if using, and serve warm.