Bring a large pot of salted water to a boil. Cook the macaroni until al dente, about 8 minutes. Drain.

Melt the butter in a large skillet over medium heat. Whisk in the flour and cook, stirring, for 1 minute until pale golden.

Reduce heat to low. Slowly whisk in the warm milk, then stir in the pumpkin puree, salt, pepper, and nutmeg. Simmer for 2 minutes.

Add the cheddar and Parmesan a handful at a time, whisking until melted and smooth.

Fold the drained pasta into the sauce. Thin with a splash of warm milk if needed. Serve right away with extra black pepper and nutmeg.