On a lightly floured surface, press the pizza crust into a rectangle. Spread a thin layer of marinara over the dough, leaving a 1/2-inch border; set aside the remaining sauce for dipping. Sprinkle the mozzarella and Parmesan evenly on top.
Evenly scatter the halved pepperoni and minced onion across the cheese, then season with Italian seasoning, garlic powder, and red pepper flakes.
Roll the dough tightly into a log, sealing the seam by pinching it together. Place the log in the refrigerator for about 10 minutes to firm up, which makes slicing easier.
Preheat the oven to 425°F (220°C) and line a baking sheet with parchment paper.
Using a serrated knife, cut the chilled log into 12 equal rolls and place them on the prepared baking sheet, leaving a little space between each.
Bake until the roll-ups are golden and the cheese is melted, about 10 to 12 minutes.
Warm the reserved marinara if desired and serve the pizza roll-ups hot alongside the sauce for dipping.