This cheesy hearty butternut squash mac and cheese is the perfect blend of tender pasta, gooey cheeses and butternut squash! It is perfect for a cozy comfort food meal , for Thanksgiving or just when you are looking for new and exciting ways of incorporating butternut squash into your dinnertime menu.

close up of mac and cheese with butternut squash in it

I originally shared this recipe on October 19, 2012. I have updated the images and some of the text today. 

Why We Love This Recipe For Butternut Squash Mac and Cheese

If you are a fan of Butternut Squash, then you probably have already had my Roasted Butternut Squash with Smoked Paprika and maybe even this Butternut Squash Lasagna. Well, today I have a brand new butternut squash recipe- this one is a Mac and Cheese and it is loaded with cooked butternut squash. And we are smitten with it!

I have added mashed squash to the cheesy creamy sauce. The sweetness of the squash with the tangy cheese, rosemary and shallot is an unbeatable combo. But then there are also tender chunks of cooked squash mixed with the macaroni to make it even better! The crunchy breadcrumb topping pushes this casserole right over the top!

Serve this delicious homemade Butternut Squash Macaroni and Cheese recipe with the other sides for your Thanksgiving Dinner, or serve it with a hearty winter salad like this Shredded Brussels Sprouts Salad with Kale!

Key Ingredients For This Recipe

the ingredients for the mac and cheese with squash with text overlay labels
  • Pasta- If you don’t want to use macaroni, feel free to use any shape of whole-grain pasta. You could also use gluten-free macaroni.
  • Butternut squash-You’ll need an entire medium-sized butternut squash, about 1 1/4 pounds.
  • Gruyere cheese-gruyere makes this a more sophisticated and gourmet mac and cheese. It’s rich, salty, nutty and super creamy. If you like cheddar better, that would work really well! I’ve tried it and it is delish!
  • Rosemary and Shallot: To Season
  • Milk-I used low fat milk for the cheese sauce, although you can whole milk for a creamier result.
  • Crunchy topping-A blend of breadcrumbs, oil, salt and paprika is sprinkled over top. It is the deal sealer.

Step-by-Step Instructions For This Recipe

coating the baking dish with cooking spray and steaming the squash

Step 1: Preheat oven

Preheat the oven to 400ºF. Coat a 2-quart baking dish with cooking spray.

Step 2: Cook squash

Meanwhile, bring several inches of water to a boil in a large saucepan fitted with a steamer attachment. Add the squash and steam, covered, until very tender 8 to 12 minutes.

mashing half the squash and boiling the macaroni

Step 3: Mash Half of the Cooked Squash

Mash about half of the squash in a small bowl and set aside.

Step 4: Meanwhile, Cook Macaroni

Meanwhile, bring a large pot of water to a boil and cook macaroni for 2 minutes less than the package instructions. Drain and set aside.

make the white sauce and then add the pasta and squash into the cheese sauce

Step 5: Make cheese sauce

Heat 1 tablespoon oil in a large saucepan over medium-high heat. Add shallot, and cook, stirring often until softened and starting to brown, 1 to 3 minutes. Add 2 cups milk and bring to a simmer. Whisk the remaining 1 cup milk, flour, mustard, rosemary, salt and pepper in a small bowl until smooth.

Whisk the flour mixture into the simmering milk, whisking constantly. Continue to cook just until the mixture bubbles and thickens. Remove from the heat.

Step 6: Assemble mac & cheese

Whisk the Gruyere cheese into the thickened milk mixture until it is melted. Add the mashed squash and whisk until combined. Stir in the macaroni and the remaining squash. Transfer to the prepared casserole dish.

topping the mac and cheese with breadcrumbs and then after it is baked

Step 7: Add breadcrumbs

Mix breadcrumbs with the remaining 1 teaspoon of oil. Add the paprika and stir until evenly moist and bright orange. Sprinkle over the macaroni.

Step 8: Bake

Transfer to the oven and bake until bubbling hot and browned on top, 10 to 15 minutes. Let cool for at least 10 minutes before serving.

serving of Healthy Butternut Squash Mac and Cheese

FAQs and Expert Tips

What to use instead of a whole butternut squash

If you can’t find any good whole squash you can buy pre-cut in the produce section or frozen butternut squash.

How long will homemade macaroni and cheese last in the fridge?

Store any leftovers in an airtight container in the fridge for up to 4 days.

Is it OK to make mac and cheese ahead of time?

Yes! Macaroni and cheese is a great make-ahead recipe. Fully assemble and store, covered, in the fridge for up to 2 days. You can freeze it for up to 2 months.

Reheating instructions

Cold macaroni and cheese that’s been made ahead might take 20 to 30 minutes to heat up. If frozen, you might need to cook at 375 degrees for 60 to 70 minutes.

Variations To Try

  • Add a protein: Add cooked chicken, sausage or bacon as a side or mixed in before baking.
  • Add more veggies: Veggies like peas, broccoli or cauliflower would taste great in this butternut squash macaroni and cheese.
  • Make it gluten-free: You can make this dish entirely gluten-free by using gluten-free pasta and gluten-free breadcrumbs.

What to Serve with Mac and Cheese

Additional Macaroni and Cheese Recipes To Try

Thanks so much for reading! If you are new here, you may want to sign up for my email newsletter to get a free weekly menu plan and the latest recipes right to your inbox. If you make this recipe, please come back and leave a star rating and review. I would love to hear what you thought!

Happy Cooking! ~Katie

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close up of mac and cheese with butternut squash in it

Butternut Squash Mac and Cheese


Description

This butternut squash mac and cheese uses an entire squash and is the perfect addition to any fall meal. Sprinkle with breadcrumbs for a crunchy topping!


Ingredients

Units Scale
  • 4 cups cubed butternut squash, about 1 1/4 pounds
  • 2 cups whole-grain macaroni, 8 oz.
  • 1 tablespoon plus 1 teaspoon avocado oil or organic canola oil, divided
  • 2 shallots, chopped
  • 3 cups low-fat milk, divided
  • 1/3 cup all-purpose flour
  • 2 teaspoons Dijon Mustard
  • 1 teaspoon chopped fresh rosemary
  • 3/4 teaspoon salt
  • 1/4 teaspoon ground white pepper
  • 6 ounces shredded Gruyere cheese, about 2 cups
  • 3 tablespoons whole-wheat panko breadcrumbs, such as Ian’s
  • 1/2 teaspoon paprika

Instructions

  1. Preheat oven to 400ºF. Coat a 2 quart baking dish with cooking spray.
  2. Meanwhile, bring several inches of water to a boil in a large saucepan fitted with a steamer attachment. Add squash and steam, covered, until very tender 8 to 12 minutes.
  3. Mash about half of the squash in a small bowl and set aside.
  4. Bring a large pot of water to a boil and cook macaroni 2 minutes less than package instructions. Drain and set aside.
  5. Heat 1 tablespoon oil in a large saucepan over medium-high heat. Add shallot, and cook, stirring often until softened and starting to brown, 1 to 3 minutes. Add 2 cups milk and bring to a simmer. Whisk the remaining 1 cup milk, flour, mustard, rosemary, salt and pepper in a small bowl until smooth. Whisk the flour mixture into the simmering milk, whisking constantly. Continue to cook just until the mixture bubbles and thickens. Remove from the heat.
  6. Whisk the Gruyere cheese into the thickened milk mixture until it is melted. Add the mashed squash and whisk until combined. Stir in the macaroni and the remaining squash. Transfer to the prepared casserole dish.
  7. Mix breadcrumbs with the remaining 1 teaspoon oil. Add the paprika and stir until evenly moist and bright orange. Sprinkle over the macaroni.
  8. Transfer to the oven and bake until bubbling hot and browned on top, 10 to 15 minutes. Let cool at least 10 minutes before serving.

Notes

Make-ahead: Macaroni and cheese is a great make-ahead recipe. Fully assemble and store, covered, in the fridge for up to 2 days. You can freeze it for up to 2 months. 

  • Prep Time: 45 minutes
  • Cook Time: 15 minutes
  • Category: Entree
  • Method: Baked
  • Cuisine: American

Nutrition

  • Serving Size: 1 generous cup each
  • Calories: 401
  • Sugar: 10 g
  • Sodium: 459 mg
  • Fat: 15 g.
  • Saturated Fat: 6 g
  • Carbohydrates: 52 g
  • Fiber: 7 g
  • Protein: 19 g

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

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