Butternut Squash Mac and Cheese

This butternut squash mac and cheese is made with a roasted butternut squash cheese sauce that’s blended until smooth and an easy breadcrumb topping for extra crunch. Bake it all in a casserole dish and serve!

You guys know we are cheese lovers (Hello, sister site Cheese Knees!). Well, we’re also butternut squash lovers which is why this butternut squash mac and cheese was a no-brainer for Fit Foodie Finds!

When testing this recipe, we tried it with steamed butternut squash and roasted butternut squash, and roasted was hands-down more flavorful. The addition of garlic and onion is essential for that bold, hearty flavor you love.

Ingredients Needed for Baked Butternut Squash Mac and Cheese

This butternut squash mac and cheese comes together with simple whole ingredients in three separate elements — the sauce, the pasta, and the breadcrumb topping.

  • Sauce: the butternut squash cheese sauce is made with roasted butternut squash, onion, and garlic. It’s blended with 2% milk, pasta water, and shredded cheese.
  • Breadcrumb topping: This is a simple bread crumb topping with savory flavors that complement the flavor of the sauce and the sage-infused pasta. You need plain bread crumbs, and some spices.
  • Pasta: This pasta is cooked to al dente in a combination of broth and water + sage and ground cloves, all of which infuse into the pasta noodles themselves for insanely amazing flavor.
butternut squash mac and cheese ingredients ready to be mixed together

Easy Substitutions + Variations

  • Pasta: We love how fun cavatappi noodles are in this butternut squash mac and cheese! Rigatoni, fusilli or penne would be great options as well.
  • Cheese: really any kind of shredded cheese works for this recipe, but we do recommend using at least half shredded cheddar. Feel free to try Gryeure or Colby Jack.
  • Swap the Butternut Squash: feel free to use another squash-like vegetable such as pumpkin or sweet potato instead of the butternut squash. You’ll still get that sweet and savory combo with those two options.
  • Add a protein: we’ve made this recipe by adding some cooked shredded chicken and it was a fantastic way to add more protein.
shredded cheese being poured in a blender

butternut squash sauce being poured over cavatappi noodles

Storage Instructions

Store this butternut squash mac and cheese in an air-tight container in the fridge for up to 3-5 days.

Reheating Mac and Cheese

The key to reheating mac and cheese is to add a little moisture (milk works great!) since the noodles continue to absorb moisture even after they’re originally cooked, and to reheat low and slow to avoid the cheese breaking down and changing texture.

Reheat in the oven

If you have time to reheat your butternut squash mac and cheese in the oven, that is a great method! Simply add a little milk (start with a tablespoon, and go up from there depending on how much mac you’re reheating!), and stir thoroughly before covering an oven-safe dish and placing in the oven at 350°F.

You’ll need 10-20 minutes of reheating time, depending on how much mac you’re reheating.

butternut squash mac and cheese in a bowl

How to Serve Butternut Squash Mac and Cheese

This mac and cheese is the perfect Thanksgiving or holiday side dish. You can eat it as a main meal or serve it as a side. If you’re looking for a protein, try our pan-fried chicken breast or sous vide steak.

mac and cheese

Butternut Squash Mac and Cheese Recipe

Butternut Squash Mac and Cheese combines classic mac and cheese with roasted butternut squash and garlic to make for the ultimate sweet and savory mac and cheese.

Prep:20 minutes

Cook:45 minutes

Total:1 hour 5 minutes

Fat 18

Carbs 55

Protein 20


Butternut Squash Mac and Cheese Sauce

  • ½ large butternut squash seeded and chopped into fourths (yields ~3 cups butternut squash puree)
  • ¾ teaspoon salt separated
  • ¼ teaspoon cayenne pepper
  • ¼ teaspoon ground pepper
  • 2 tablespoons olive oil separated
  • ½ large white onion diced
  • 4 cloves garlic peeled
  • 1 cup 2% milk
  • 2 cups pasta water depending on how much you need
  • 2 cups shredded cheddar cheese
  • 2 cups shredded mozzarella cheese



  • Preheat the oven to 400ºF and spray a baking sheet with non-stick cooking spray. 

  • Combine 1/2 teaspoon salt, cayenne pepper, and pepper into a small bowl. Set aside. 

  • Place the butternut squash on the baking sheet and drizzle the butternut squash with 1 tablespoon olive oil and season with the spices. Rub the olive oil and spices into the butternut squash. Then, move the squash to one side of th baking sheet. 

  • Place the white onion and the garlic cloves on the other side of the baking sheet. Drizzle with the other tablespoon of olive oil and the remaining ¼ teaspoon of salt. 

  • Place the baking sheet into the oven and roast for 20 minutes. Then, remove the garlic and onions so that they do not burn and flip the butternut squash over. Roast for another 20-30 minutes or until the butternut squash is fork-tender.

  • Prepare the pasta while the butternut squash is baking. Add the broth, water, sage leaves, salt, and cloves to a large pot. Bring to a boil. Add the pasta to the boiling water and cook until just a little under al dente (it will continue to cook in the oven). 

  • Remove 2 cups of the pasta water (discarding the sage leaves) from the pot and set aside. Then, strain the pasta from the water and rinse the noodles with cold water. Set aside. 

  • Prepare the breadcrumb topping. Heat a small skillet pan over medium heat and add all of the bread crumb topping ingredients to the skillet and mix the ingredients together. Toast the bread crumbs until golden brown, about 4-5 minutes. Remove from heat and set aside. 

  • Remove the butternut squash from the oven when it is fork tender. Use a spoon to carefully peel the skin off the butternut squash (it should come off easily). 

  • Place the butternut squash, onion, garlic, and 1 cup of the pasta water into a high speed blender and blend until smooth. Add the cheddar cheese to the blender and blend until melted and combined. Next, add the Italian cheese blend to the blender and blend until smooth and melted. Finally, add the 2% milk to the blender and blend until thick and creamy. If your sauce is too thick, you can add more pasta water by the tablespoon.

  • Turn the oven to broil and spray a 9×13-inch casserole dish with cooking spray. 

  • Add the noodles to the casserole dish and pour the butternut squash cheese sauce over the noodles and mix until combined. Sprinkle the bread crumb topping over the pasta. You can use all of it or as much as you would like. Place the casserole dish into the oven.

  • Broil the mac and cheese until the top is golden brown (2-3 minutes).

  • Remove from the oven and garnish with freshly chopped sage leaves. 

Tips & Notes

  • You remove the onions halfway through the cook time to be sure the onions don’t burn.  
  • If your sauce is too thick, you can add more pasta water by the tablespoon.

Nutrition facts

Calories: 445kcal Carbohydrates: 55g Protein: 20g Fat: 18g Fiber: 5g Sugar: 8g

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