Set a separate large saucepan to medium-high heat. Add butternut squash, chicken broth, and milk. Season with salt and pepper. Bring to a simmer. Reduce heat to low, cover and cook until squash is tender, about 15 minutes, stirring occasionally. Add squash mixture to a blender and purée until smooth, or purée in the saucepan with an immersion blender. Pour purée into a bowl.
With the squash set aside, set same saucepan over medium heat. Add butter, squash purée and nutmeg. Simmer and cook until thickened, about 5 minutes. Remove from heat. Add cheese and stir to combine.
Meanwhile, add macaroni to boiling water and cook about 8 minutes, or until al dente.
Add the pasta to saucepan with squash-cheese mixture; mix well. Serve warm.
Adapted from Daphne Oz
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