Heat olive oil or butter in a cast iron skillet over medium-high. Add diced onions, bell peppers, Italian seasoning, basil, salt, and pepper.
Cook 3–4 minutes, stirring occasionally, until soft and fragrant. Set aside.
Spread 2–3 tablespoons of marinara on 4 tortillas, leaving a ½-inch border. Layer with sautéed veggies, pepperoni, and mozzarella.
Top each with another tortilla. Press down gently to help seal.
Heat the skillet over medium. Cook each quesadilla for 2–3 minutes per side until golden and the cheese is melted.
Cool for 1 minute. Slice into wedges and serve hot.