Gather the ingredients.
Cook the macaroni in boiling salted water following package directions. Drain and then set aside.
Heat the oven to 350 F.
Grease a 2 1/2- to 3-quart casserole.
Heat the olive oil in a large saucepan or saute pan over medium heat. Crumble the sausage and add it to the pan along with the bell pepper and onion; cook, stirring and breaking up sausage, until sausage is no longer pink and vegetables are tender. Spoon off any excess grease and add the seasoning, pepper flakes, black pepper, and garlic.
Add the flour to the sausage mixture and cook for about 2 minutes longer, stirring constantly. Gradually stir in the milk. Continue cooking until thickened, stirring constantly. Stir in the cheeses and add salt, to taste.
Fold the macaroni and tomatoes into the sausage and sauce mixture. Spoon into the prepared casserole.
Combine the bread crumbs with melted butter and sprinkle over the casserole.
Bake the for 25 minutes.
Increase heat to 400 F and bake for 5 to 10 minutes longer, until crumb topping is lightly browned.