Bring a large pot of salted water to a boil. Add pasta and cook until al dente (8-10 minutes). Reserve 1 cup of pasta water, draining the rest. Set aside.
To a large Dutch oven (13-quart) or heavy bottom pot over medium heat, add andouille sausage. Cook until browned, 7-9 minutes, stirring frequently.
Once done, remove the andouille from the pot. Set aside.
To the pot, add onion and pepper. Cook until softened, about 3-5 minutes, stirring occasionally. Add the minced garlic and cook for one more minute. Remove from the pot. Set aside with the andouille.
In the pot, melt the butter, and stir, scraping up the browned bits in the pan. Add the flour and whisk constantly for 1-2 minutes.
Gradually pour in the milk, whisking constantly for 3-5 minutes, or until the mixture is thickened.
Add Cajun seasoning. Stir to combine.
Remove from heat. Add both cheeses and ½ cup of reserved pasta water. Stir to melt the cheese.
Add the cooked pasta, andouille, and cooked vegetables. Stir to combine. Add more pasta water, as needed, to reach your desired consistency.
Serve immediately, garnished with chopped parsley.