Preheat the oven to 375°F (190°C).
Add a large pinch of salt into a pot of boiling water. Add the macaroni and cook according to package directions or until al dente. Drain well.
Over medium-high heat, melt ¼ cup of butter in a large pot. Once the butter has melted add ¼ cup of flour. Stir constantly. Cook over low heat for 2-3 minutes, continue to whisk until the consistency becomes thick and pasty.
Add the milk very gradually in stages. Whisk constantly allowing the milk to thicken, then add a little more milk at a time while stirring constantly.
Continue to whisk as the sauce thickens.
Take the sauce off the heat and add in the cheese. Stir until the cheese has melted and the sauce is smooth. Add in the salt, pepper, and nutmeg. Mix to combine.
Add in the cooked macaroni and stir so all the pasta is coated with the cheese sauce. Pour the mixture into a 9 x 9 casserole dish.