Preheat the oven to 350°F.
Bring a large pot of salted water to a boil. Add the shell pasta and cook it until al dente, about 10 minutes. Drain the pasta and set it aside.
Add the olive oil to a large heavy-bottomed stock pot set over medium-low heat. Once the oil is warm, add the diced onions, diced green peppers, and a pinch of salt and pepper and cook, stirring constantly, until the onions are translucent. Add the Italian sausage and cook, breaking apart the sausage with a spatula, until the sausage is browned and cooked throughout.
Reduce the heat to low and add the tomato sauce then add the cooked pasta to the pot, along with 1/2 cup of the sliced pepperoni and stir to combine.
Transfer half of the pasta to a 9x13-inch baking dish, top it with half of the shredded mozzarella cheese, then repeat another layer of the pasta, the remaining cheese and the remaining 1/4 cup of pepperoni.
Bake the pasta for about about 15 minutes or until the cheese is melted. Remove the baked pasta from the oven and serve.
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