Preheat the oven to 400°F (200°C).
Using a sharp knife, cut a deep pocket into the side of each chicken breast without slicing all the way through.
In a mixing bowl, combine the mozzarella cheese, pizza sauce, chopped pepperoni, Parmesan cheese, basil, and crushed red pepper flakes if using.
Spoon the filling evenly into each chicken breast and secure the openings with toothpicks or kitchen twine.
Season both sides of the chicken with garlic powder, onion powder, Italian seasoning, paprika, salt, and black pepper.
Heat the olive oil in a large oven-safe skillet over medium-high heat.
Sear the stuffed chicken breasts for 3 to 4 minutes per side until golden brown.
Transfer the skillet to the oven and bake for 15 to 18 minutes, or until the chicken reaches an internal temperature of 165°F (74°C).
Remove the chicken from the oven and let it rest for 5 minutes.
Remove the toothpicks or kitchen twine, slice if desired, and serve with extra warm pizza sauce.