Preheat the oven to 375°F. First, cut the chicken breasts in half lengthwise, about ⅔rds of the way through. In a large bowl, toss the chicken with olive oil, salt, pepper, and the seasonings. Make sure to coat the insides of the chicken as well.
In a deep casserole dish, spread some of the marinara sauce evenly on the bottom. Add some of the basil and fresh oregano.
Add some of the sauce, fresh mozzarella, parmesan, basil, and pepperoni inside each of the chicken breasts and place them inside the casserole dish. Close the chicken and top with more marinara sauce and basil. Add more sauce, mozzarella, parmesan, and pepperoni on top of each chicken breast.
Insert an oven-safe meat thermometer into a piece of chicken. Bake at 375°F until the internal temperature reaches 165°F, about 40 minutes. Once cooked, broil for 3-5 minutes until the top is crispy and golden brown. Remove and let rest for 5-8 minutes.
Garnish with basil, parmesan, salt, pepper, and more red pepper flakes if desired. Enjoy!
You can store these leftovers in the casserole dish, covered with saran wrap or aluminum foil in the fridge for up to 3 days. You can also store individual portions in an airtight container. Reheat in the oven with low heat or in the microwave.