Preheat the oven to 400°F. Cook the macaroni according to the package directions. Drain and set aside.
In a large saucepan, melt the butter over medium heat. Add the sausage and cook until browned, one to two minutes per side. Remove and set aside.
In the same pan, add the onion and pepper. Cook until tender, four to five minutes. Add the garlic and cook for one minute longer.
Sprinkle the flour over the mixture and stir until well combined. Gradually add in the milk and cook until thickened, three to four minutes, stirring occasionally. Add the shredded cheddar, pepper jack and Parmesan cheeses, Cajun seasoning, salt and pepper. Stir until the cheese has melted. Stir in the cooked macaroni and sausage.
Transfer the mixture to a greased 13x9-inch baking dish. Bake until the cheese is bubbly and the edges are golden brown, 20 to 25 minutes.
