Gather all ingredients. Preheat the oven to 375 degrees F (190 degrees C).
Bring a large pot of water to a boil. Cook pasta 2 minutes less than package directions. Drain and rinse with cold water until cool.
Meanwhile, heat a large skillet over medium heat. Add Italian sausage, onion, bell pepper, and garlic; cook and stir until sausage is browned and fully cooked.
Add marinara sauce, Italian seasoning, and crushed red pepper, if using. Cook over medium heat for 10 minutes, stirring occasionally, to meld flavors.
Spread 2 cups sauce in the bottom of a 9x13-inch baking dish.
Combine cottage cheese, 1 cup mozzarella cheese, 1/4 cup Parmesan cheese, and parsley in a bowl.
Divide cheese mixture between pasta shells, stuffing with 1 scant tablespoon per shell.
Arrange shells evenly over sauce in the baking dish.
Spoon remaining sauce over shells and sprinkle with remaining mozzarella and Parmesan cheese.
Bake, uncovered, until cheese is melted and sauce is bubbly, 25 minutes. Tent loosely with foil if it starts to get overbrowned.
Garnish with additional parsley.
