Begin by bringing a large pot of salted water to a boil. Add the pasta and cook it according to the package directions.
While the pasta is cooking, heat a saucepan or pot over medium heat. Add the butter and let it melt. Then whisk in the flour and cook for 1 to 2 minutes until it starts to bubble and turns golden.
Pour in the half and half while whisking continuously until the mixture is smooth. Add the dry mustard powder, garlic powder, black pepper, nutmeg, cayenne powder (if using), and salt. Whisk everything together.
Reduce the heat to low and add all the cheeses. Keep whisking until the sauce is smooth and free of any clumps.
Once the pasta is cooked, drain it and add it to the sauce. Mix everything together until the pasta is well coated.
Serve your homemade Panera Mac & Cheese warm and enjoy the deliciousness!