Preheat the oven to 375°F (190°C).
In a large skillet over medium-high heat, sauté the ground beef and diced onions until the beef is fully browned and the onions are translucent. Drain any excess rendered fat.
Add minced garlic, oregano, salt, and black pepper to the skillet; cook for 60 seconds until fragrant.
Incorporate 0.5 cup of marinara sauce and 0.5 cup of shredded mozzarella into the beef mixture, stirring until the cheese is partially melted.
Spread 0.5 cup of marinara sauce evenly across the bottom of a 9x13 inch baking dish.
Distribute the beef mixture evenly among the 12 flour tortillas. Roll each tortilla tightly and place them seam-side down in the baking dish.
Pour the remaining 1 cup of marinara sauce over the center of the rolled tortillas.
Evenly distribute the remaining 1.5 cups of mozzarella cheese, sliced pepperoni, and grated Parmesan over the top.
Bake for 20 to 25 minutes, or until the cheese is bubbling and slightly golden brown.
Allow the dish to rest for 5 minutes before serving to ensure internal structural integrity.