Cook pasta in a large pot of boiling salted water until al dente. Drain in a colander.
Melt the butter in a large saucepan. Add the onion and saute until tender, about 3 minutes. Season with salt and pepper. Add flour and stir until it looks pasty and reaches a golden blonde color, about 2 minutes.
Slowly whisk in the warm milk, bringing up to a simmer, and allow the mixture to thicken. Stir in the mustard. Let simmer on low heat for 5 minutes, until thick enough to coat the back of a spoon.
Gradually stir in the cheese a handful at a time. Stir in the pasta, making sure it's all covered with the cheese sauce and serve hot.