Cook pasta as directed on the packaging until it’s al dente. Drain and set aside.
While the pasta is cooking, melt butter in a large skillet over medium heat. Once melted, whisk in the flour, and cook for 1 minute. Then slowly whisk in milk. Continue whisking until the sauce thickens. Once it’s thick enough to coat the back of a spoon, for about 2 minutes, reduce heat to medium-low.
Mix in the pumpkin puree, then the cheddar and gruyere cheese. Add the nutmeg, salt and pepper to taste.
Add pasta to the sauce, tossing until it’s well coated. If the sauce is too thick, add pasta water or more milk