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Butternut squash mac and cheese is a flavorful and delicious fall twist on a classic, with a rich and creamy sauce that is secretly loaded with veggies. |

Butternut Squash Mac and Cheese

  • Author: Sam Hu | Ahead of Thyme
  • Total Time: 15 minutes
  • Yield: 4-6 servings
  • Diet: Vegetarian


Butternut squash mac and cheese is a flavorful and delicious fall twist on a classic, with a rich and creamy sauce that is secretly loaded with veggies.


  • 1 lb. pasta, shells or elbow
  • 2 tablespoons butter
  • 2 tablespoons all-purpose flour
  • 2 cups whole milk
  • 1 + 1/4 cup butternut squash puree, store-bought or homemade*
  • 2 cups sharp cheddar cheese
  • 1/4 teaspoon paprika
  • 1/2 teaspoon salt
  • 1/4 teaspoon ground black pepper


  1. Bring a large pot of salted water to a boil over high heat. Add pasta and cook until al dente, about 8-10 minutes. Reserve one cup of the pasta water and drain the rest in a colander.
  2. Heat butter in another large pot over medium heat. Add flour and whisk to combine, about 1 minute. Pour in half the milk and whisk until there are no clumps. Then, add the remaining cup of milk and whisk to combine.
  3. Whisk in butternut squash puree. If the butternut squash is too chunky, use an immersion blender to blend the sauce until smooth. Stir in cheese until it has melted. Season with paprika, salt, and pepper.
  4. Add the drained pasta and toss together. Add more seasoning if needed, to taste.


* Make homemade butternut squash puree: Preheat oven to 350°F. Cut a medium butternut squash in half lengthwise and scoop out the seeds. Lightly brush the cut sides with olive oil. Place on a quarter sheet baking pan cut side up and bake 1 hour or until very tender. Scoop out the flesh of the butternut squash and place in a large mixing bowl. With a potato masher, mash until smooth. If the butternut squash is too chunky for your liking, transfer it to a blender and puree it until desired consistency is achieved.

How to store: After allowing the butternut squash mac and cheese to cool, place any leftovers in an airtight container and store in the refrigerator for up to 3-4 days.

How to freeze: Mac and cheese is a great freezer-friendly food. Portion and freeze it in meal prep containers or freezer bags and label it. Freezer for up to 3 months.

How to reheat: If frozen, thaw mac overnight in the fridge first. Then, reheat in the microwave, covered on medium heat in 30-second intervals, stirring in between. You can also reheat on the stove over medium-low heat until warmed through. Add a splash of water if the mac and cheese has thickened too much when stored.

  • Prep Time: 5 minutes
  • Cook Time: 10 minutes
  • Category: Pasta
  • Method: Stovetop
  • Cuisine: American

Keywords: butternut squash mac and cheese, mac and cheese with butternut squash, butternut squash pasta, macaroni and cheese