Preheat oven to 375°F (190°C). Grease a 9x13-inch baking dish with cooking spray or olive oil.

In a large skillet over medium-high heat, brown the ground beef with the diced onion and bell pepper for 7-8 minutes until meat is no longer pink and vegetables are tender. Drain excess grease if needed.

Reduce heat to medium. Add minced garlic, Italian seasoning, red pepper flakes if using, salt, and black pepper. Cook for 1-2 minutes, stirring constantly, until fragrant.

Pour the marinara sauce into the skillet and stir to combine with the meat mixture. Let simmer for 2-3 minutes, stirring occasionally. Taste and adjust seasoning if needed.

Pour half of the meat and sauce mixture into the prepared baking dish, spreading evenly. Sprinkle with half the mozzarella (1.5 cups) and half the Parmesan (1/4 cup). Arrange half the pepperoni slices over the cheese.

Spread the remaining meat mixture over the pepperoni layer. Top with remaining mozzarella and Parmesan, distributing evenly. Arrange remaining pepperoni slices on top.

Bake for 20-25 minutes until cheese is melted and bubbly with edges starting to brown. Pepperoni should curl and develop crispy spots. For extra browning, broil for 2-3 minutes at the end, watching carefully.

Remove from oven and let rest for 5 minutes before cutting into portions. This allows cheese to set slightly for cleaner serving.