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Butternut Squash Mac and Cheese
Welcome to the best ever butternut squash mac and cheese!
It’s a creamy three-cheese mac with a creamy butternut squash sauce tossed with cavatappi noodles.
It’s cozy, cheesy fall-inspired comfort food!

How to make butternut squash mac and cheese
Featured Ingredients
- Butternut squash: You can roast or steam a whole, peeled and seeded squash or steam a bag of frozen squash.
- Either way, the cooked squash will be pureed with plain Greek yogurt, milk, stock and spices then simmered with cheese.
- Pasta: I use twirly cavatappi, but any tubular pasta works perfectly.
- You want to make sure there is sauce inside the noodle, of course!
- Greek yogurt: Plain Greek yogurt will add richness, creaminess and a boost of nutrition to the sauce.
- Milk and stock: The milk adds creaminess and the stock adds flavor.
- Spices: Nutmeg, cayenne, salt and black pepper, to be exact.
- Trust me, this combo is fabulous in a cheese sauce.
- Butter: A few tablespoons for creamy saltiness.
- Cheeses: I like a combination of cheddar, Gruyere and Parm.
- Breadcrumbs: Panko, for ultimate light crispiness for the topping.
- Parsley: Optional, but adds freshness and color.

Step-by-Step Instructions
- Preheat oven to 375 degrees.
- Cut butternut squash in half, lengthwise, and scoop out seeds.
- Place in baking dish, flesh side down, and pour water in the baking dish.
- Roast in oven for 35-40 minutes, until soft.
- Scoop out cooked flesh and discard skin.ย ย Set squash flesh aside.
- Cook pasta according to package directions, omitting salt.ย Drain and set aside.
- Meanwhile, place butternut squash, Greek yogurt, milk, chicken broth, salt, black pepper, nutmeg and cayenne in a blender and puree until smooth.
- (If the squash is still hot, remove plastic cap from blender lid and place a kitchen towel over it so steam can escape and the hot contents donโt explode.)
- Heat butter in a saucepan and add squash puree.
- Add marble jack, Gruyere and half of the Parmesan cheese and cook on medium, stirring, until cheese is melted.
- Taste and adjust seasoning, if necessary.
- Coat a 13×9 baking dish with cooking spray.
- Add cooked pasta to the baking dish and pour in the squash/cheese sauce.
- Stir until combined.ย Place in oven and bake for 20 minutes.
- Remove dish and turn oven on low broil.ย Top pasta with remaining Parmesan cheese and bread crumbs.ย Spray top with cooking spray.
- Place back in the oven and broil for 4-5 minutes, until top is browned, rotating the dish if necessary.
- Remove from the oven and sprinkle with parsley (if using).

Recipe Substitutions and Alterations
- Instead of butternut squash: Try canned pumpkin or sweet potato (or butternut squash).
- You could also use another winter squash, like acorn.
- Instead of cavatappi: Use any tubular pasta.
- Instead of Greek yogurt: Use more milk.
- For the milk: Use low-fat or whole milk.
- For the stock: Use vegetable or chicken.
- For the cheeses: Use any combination of your favorite melty cheeses.

Nutrition Considerations
- To make this gluten free: Use gluten free pasta and breadcrumbs.
- Be sure all other ingredients are gluten free.
- To make this nut free: This recipe does not contain nuts.
- Be sure all packaged ingredients are nut free.
- To make this egg free: This recipe does not contain nuts.

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Butternut Squash Mac and Cheese
Creamy 3-cheese mac with a creamy butternut squash sauce tossed with cavatappi noodles.
- Prep Time: 20-25 mins
- Cook Time: 1 hr-1 hr 5 mins
- Total Time: 1 hr 20 mins or 1 hr 25 mins
- Yield: Serves 8
- Category: Pasta
- Method: Stove-Top, Baking
- Cuisine: American
- Diet: Vegetarian
Ingredients
Scale
- 1 large butternut squash, about 3 pounds*
- ยผ cup water
- 1-pound cavatappi or other tubular pasta
- 3 tablespoons plain Greek yogurt
- 1 ยฝ cups milk
- 1 ยผ cups unsalted vegetable or chicken stock
- 2 teaspoons coarse salt
- ยฝ teaspoon ground black pepper
- ยผ teaspoon ground nutmeg
- ยผ teaspoon cayenne pepper
- 3 tablespoons butter
- 2 ยฝ cups shredded cheddar cheese
- ยฝ cup shredded Gruyere cheese
- ยฝ cup freshly shredded Parmesan cheese, divided
- ยฝ cup panko breadcrumbs
- ยผ cup chopped fresh parsley (optional)
Instructions
- Preheat oven to 375 degrees.ย ย Cut butternut squash in half, lengthwise, and scoop out seeds.ย ย Place in baking dish, flesh side down, and pour water in the baking dish.ย ย Roast in oven for 35-40 minutes, until soft.ย ย Scoop out cooked flesh and discard skin.ย ย Set squash flesh aside. Alternatively, steam a 10-12 ounce bag of frozen butternut squash cubes.
- Cook pasta according to package directions, omitting salt.ย Drain and set aside.
- Meanwhile, place butternut squash, Greek yogurt, milk, chicken broth, salt, black pepper, nutmeg and cayenne in a blender and puree until smooth. (If the squash is still hot, remove the plastic cap from blender lid and place a kitchen towel over it so steam can escape and the hot contents donโt explode.)
- Heat butter in a saucepan and add the squash puree.ย Add the cheddar, Gruyere and half of the Parmesan cheese and cook on medium-low, stirring, until cheese is melted. Taste and adjust the seasoning, if necessary.
- Coat a 9×13 baking dish with cooking spray. Add cooked pasta to the baking dish and pour in the squash/cheese sauce.ย Stir until combined.ย Place in oven and bake for 20 minutes.
- Remove the baking dish from the oven and set the oven on a low broil.ย Top pasta with remaining Parmesan cheese and bread crumbs.ย Spray top with cooking spray.ย Place the baking dish back in the oven and broil for 4-5 minutes, until top is browned, rotating the dish if necessary.
- Remove from the oven and sprinkle with parsley (if using).
Notes
Cooking Tip: You can cook the squash up to 3 days in advance. You can also use 2 10 ounce bags of frozen cubed squash; thaw and place into the blender and puree with the other sauce ingredients.
Nutrition
- Serving Size: 1/8 of recipe
- Calories: 459
- Sugar: 6g
- Sodium: 477mg
- Fat: 18g
- Saturated Fat: 10g
- Unsaturated Fat: 8g
- Trans Fat: 0g
- Carbohydrates: 56g
- Fiber: 4g
- Protein: 21g
- Cholesterol: 52mg


Thanks, Bonnie! I hope you enjoy it ๐
Made this for Thanksgiving – thanks to you! It was a HUGE hit! I made it with gf noodles and gf breadcrumbs!
Awesome idea!! Glad you loved it!
I love the idea of blending in the squash!! I usually add a layer of chopped butternut squash to the top of my baked mac and cheese but that is not always a huge hit with guests. I will be trying this recipe for Christmas!!
I hope your family enjoys the recipe, Molly! Happy Holidays!
This looks incredible! My sister makes a version of mac and cheese with yams that she swears by. I will have to try this one.
Pinned!
Hi Kristen! The butternut squash makes such a creamy and colorful sauce! It’s magnificent and I hope you enjoy it ๐
Julie
It was delicious!!
Yay! So glad you loved it, Haley!!