This one-pot butternut squash mac and cheese is easy to make, delicious, and a great way to add more veggies to your diet. Whether you’re enjoying it as a main course or a side dish, this tasty recipe is something the whole family is sure to love and a little something that you can add to your healthy comfort food recipe repertoire.

Butternut squash in mac and cheese? Yes, you read that right. Although it’s not traditional, or anything like boxed mac and cheese, the soft, sweet, orange flesh of winter squash makes a lovely addition to a cheese sauce. Not only does the squash puree make the mac and cheese extra rich and creamy, but it also adds a lovely boost of fiber and micronutrients, which is something that we can all use a little more of.
What You’ll Need
You’ll need the following ingredients to make my fiber-packed mac and cheese:
- Butternut Squash: You can buy a whole butternut squash, peel and cut it yourself, buy pre-cubed squash, or use frozen butternut squash, see the note below.
- Short-Cut Pasta: You can use any variation of short-cut pasta you like, such as gomiti or elbow macaroni, cavatappi or corkscrew pasta, conchiglie or shell pasta, penne, or fusilli. I used pipe rigate, also known as small snail pasta, for my recipe. You can also use whole wheat pasta if preferred.
- Cheese: I think a combination of sharp cheddar cheese and gruyere provides the best texture and flavor. If you can’t find gruyere cheese you can replace it with additional cheddar, just make sure you use the good stuff since cheese is the star of this mac and cheese show.
- Butter: To add some creaminess and fry the sage.
- Milk: To help create the cheese sauce, whole milk or 2% milk work best.
- Onion Powder: To add some flavor.
- Garlic Powder: To add a bit more flavor.
- Salt: To season the dish.
- Fresh Sage: While optional, fresh sage helps to elevate the flavors and make a great topping to the dish.
While optional, you can also add a pinch of smoked paprika for additional flavor and color.
Dietary Adaptions
To Make it Gluten-Free: Use short-cut gluten-free pasta instead of wheat-based pasta.

How to Make Butternut Squash Mac and Cheese
Once you’ve got the ingredients, here’s how you’ll assemble them:
- Roast the squash. Roasting the squash adds a depth of flavor. (If you want to skip this step, you can use a can of squash puree.)
- Puree the squash. Blend the squash into a rich and creamy puree.
- Boil the pasta. Cook the pasta to your liking, I think al dente is best.
- Fry the sage (optional). While this isn’t a must, it really does elevate the flavors.
- Make the sauce. Mix the butter, spices, squash, milk, and cheese to make the quintessential butternut squash cheese sauce.
- Mix the pasta and sauce. Once the sauce is ready, gently fold in the pasta, until well combined, smooth, and creamy.
And that’s it! If you like breadcrumbs on your make and cheese (it’s just not my thing), simply add the completed dish to a large baking dish, sprinkle with breadcrumbs, and bake in the oven at 350°F for 10-15 minutes until golden and crispy.
Cheese Sauce Troubleshooting:
- If your cheese sauce is too thick, you can thin it with a bit of additional milk.
- If your cheese sauce is too thin, you can thicken it with a bit of all-purpose flour.

Red’s Nutrition Tip
If you think pasta is unhealthy, think again! Pasta is a healthy food, that has been consumed across cultures for thousands of years, and a source of complex carbohydrates and fiber that can be included in a healthy and balanced diet along with proteins, fats, and nutrients.

What does butternut squash mac n cheese taste like?
Mac and cheese with butternut squash tastes very similar to regular mac and cheese with a slightly sweeter and nuttier taste. While the flavor is slightly different, the texture is essentially the same.
Is it better to boil or roast butternut squash for mac and cheese?
Many squash mac and cheese recipes will call for boiling the squash for the sauce, but roasting it provides much more flavor. Although boiling the squash is quicker, you will lose flavor, texture, and a little nutrition in the process, so it’s well worth the extra time and effort for the flavor roasting the squash will provide.
Can I use frozen butternut squash?
Yes. Simply add the frozen butternut squash to the baking sheet and cook as per the directions. You may need to add an additional 5 minutes or so to ensure the squash is fully cooked through, just use a fork to check for doneness and add additional cooking time as needed.
Can I use another type of squash?
Yes, you can easily substitute the butternut squash for another type of hard winter squash, such as buttercup, acorn, or hubbard squash. Just don’t use spaghetti squash as the texture is not the same.

What to Serve with Squash Mac and Cheese
This mac and cheese is rich in carbohydrates and fat, with a decent amount of fiber, so pairing it with protein and additional veggies can make it a more balanced meal.
To add protein: Serve it with roasted, grilled, or baked chicken, such as my lemon paprika chicken, a bit of sausage, or steak.
To add vegetables: Serve it with steamed or roasted broccoli, asparagus, green peas, or spinach, or add them right into the dish.

Storage + Reheating
To Store: Allow the mac and cheese to cool completely, then transfer to airtight containers and store in the fridge for up to 3 days.
To Freeze: Once cooled, transfer to an airtight container and store in the freezer for up to 3 months.
To Reheat: This squash mac and cheese is best reheated in a pan or pot on low heat. Simply add the leftovers to the pot with a little bit of water or milk and warm, stirring consistently and adding additional milk or water as needed, until the sauce is smooth and creamy. Alternatively, it can be reheated in the microwave in a microwave-safe container for 1-2 minutes. If frozen, be sure to thaw before reheating.
More Butternut Squash Recipes:
Print
Butternut Squash Mac and Cheese
Ready in under an hour, this butternut squash mac and cheese is a healthy comfort-food dish the whole family will love. It also keeps well in the fridge and freezer so it makes great leftovers too.
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Prep Time: 10 minutes
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Cook Time: 40 minutes
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Total Time: 50 minutes
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Yield: 6 servings 1x
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Category: Mains
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Method: Stovetop
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Cuisine: American
Ingredients
- 1 pound cubed butternut squash (about 5 cups)
- 1 pound short-cut pasta, such as elbows, penne, or shells
- 1 tablespoon olive oil
- 2 tablespoons butter
- 1 teaspoon onion powder
- 1 teaspoon garlic powder
- 1 pinch smoked paprika (optional)
- 1 cup milk, 2% or whole, plus more as needed
- 4 ounces sharp cheddar cheese, grated (about 1 1/2 cups)
- 4 ounces Gruyère cheese, grated (about 1 1/2 cups)
- 8 fresh sage leaves (optional)
- Salt
- Black pepper
Instructions
- Preheat the oven to 400°F.
- Place the cubed butternut squash on a baking sheet lined with parchment paper, drizzle with olive oil, and season generously with salt and pepper. Toss the butternut squash on the baking sheet, using your hands, until well coated, and then transfer to the oven to bake for 30 minutes or until tender and easily pierced with a fork.
- When the butternut squash is almost cooked, fill a large pot with water, season with salt, and bring to a boil. Once the water is boiling, add pasta and cook to al dente or until tender as per package directions.
- While the pasta is cooking, transfer the roasted butternut to a food processor or blender and purée until creamy and smooth, and grate all of your cheese on a cutting board.
- Once the pasta has cooked, drain the pasta into a colander and set it aside for a moment.
- In the same pot used to cook the pasta, add the butter and allow it to melt on medium heat. (Optional: Once the butter has melted, add the fresh sage leaves and fry for 30 seconds to 1 minute per side until crispy, then remove from the pan, season with a pinch of salt, and set aside.)
- Add the garlic powder, onion powder, smoked paprika, and a generous pinch of salt, and some black pepper to the pan with the melted butter and heat for about 10 seconds, then add butternut squash purée and 1 cup of milk and whisk to combine.
- Reduce the heat to low and then add the grated cheese, whisking the mixture constantly until the cheese is all melted and a sauce has formed. (If you find the sauce too thin, simply add a sprinkle of all-purpose flour to thicken it up.)
- Once the sauce is ready, return the cooked pasta to the pot and toss gently to combine with the butternut squash cheese sauce until the pasta is well coated, adding additional splashes of milk as needed to help the cheese sauce coat the pasta.
- The mac and cheese can be served immediately with a sprinkle of the fried sage, any leftovers can be cooled and stored in the fridge for 3 days or in the freezer for 3 months.
Nutrition
- Serving Size: 1 serving
- Calories: 551 calories
- Sugar: 6 grams
- Fat: 21 grams
- Carbohydrates: 60 grams
- Fiber: 5 grams
- Protein: 22 grams
This was soo delicious ! Wondering what would count as a serving just for my macros because I absolutely ate two! Lol
My wife and I enjoyed this dish!
Happy you enjoyed it, thanks for sharing, Ronnie!
Love this! (And it was a hit with the kids too!) Easy to prep in advance earlier in the day, and then easy to put the sauce all together
I’m so happy to hear it and love when a recipe is kid approved! Thank you for sharing, Adrienne.
Just enjoyed this dish for dinner tonight. It was delicious. I did find I had to add more milk than what was stated. A definite make again.
Thanks for sharing and for the tip! 🙂