Preheat your oven to 375°F (190°C) and grease a 9x9 inch baking dish with non-stick spray or olive oil.
On a clean surface, unroll the refrigerated pizza dough and cut it into small squares (about 1½ inches each).
In a large bowl, combine the chopped pepperoni, shredded mozzarella cheese, Italian seasoning, garlic powder, and crushed red pepper flakes if using. Mix well to combine.
Take each dough square, place a spoonful of the cheese and pepperoni mixture in the center, and pinch the corners together to form a ball. Repeat until all ingredients are used.
Lightly brush the bottom of the prepared baking dish with olive oil. Arrange the cheese-stuffed dough balls in a single layer, making sure they are close together but not overcrowded.
Pour the marinara sauce evenly over the rolls. If desired, sprinkle additional cheese or herbs on top for added flavor.
Cover the baking dish with aluminum foil and bake in the preheated oven for 20 minutes.
Remove the foil and bake for an additional 10-15 minutes, or until the tops are golden brown and the cheese is bubbly.
Once baked, remove from the oven and let it cool for a few minutes.
Garnish with fresh parsley before serving with extra marinara sauce on the side for dipping.