Preheat the oven to 350°F. Spray a 13x9-inch baking dish with cooking spray.
In a large skillet, cook sausage until browned and crumbled.
Push browned sausage to the side and add onion and garlic to skillet. Turn heat to medium and cook 2-3 minutes. Add pizza sauce and Italian seasoning, mixing everything together well. Simmer until sauce is reduced and thickened.
Turn off heat and let mixture cool a few minutes. Then add chopped pepperoni and 1 ½ cups shredded mozzarella, stirring gently to combine.
Fill each pepper with meat mixture and add to baking dish. Bake 20 minutes.
Remove from oven and top with remaining mozzarella cheese. Return to oven and bake an additional 25 minutes, or until cheese is nicely browned and peppers are soft.