Butternut Squash Macaroni and Cheese

5 from 6 votes
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You’d never guess that this creamy and kid-friendly Butternut Squash Mac and Cheese is packed with veggie power! It’s a rich and cheesy pasta casserole recipe that puts a delicious, gluten-free spin on classic macaroni and cheese.

Butternut squash macaroni and cheese served in a bowl with a blue and white fork.

I began making this recipe when my son entered preschool. He’s always eaten foods at school that I could never convince him to eat at home, like green beans! Let’s face it, little ones can be picky eaters. And back then, I often had to get creative with sneaking vegetables into our family meals.

Enter this ultra creamy and easy recipe for macaroni and cheese with all its familiar tangy and cheesy flavor. However, the sauce is made with a secret ingredient: fresh butternut squash. Not only is this pasta recipe gluten free, but it’s been a surefire way of getting my kids to actually enjoy their veggies throughout the years. I just know your family will love it, too!

Why You’ll Love This Butternut Squash Macaroni and Cheese Recipe

  • Flavorful. This butternut squash version is not quite as cheesy and gooey as your traditional macaroni and cheese, but it is still delicious and creamy, and full of flavor! The sauce is fresh and light, with sweet-savory butternut squash, broth, cheese, and tangy mustard.
  • Creamy, without the cream. Extra sharp cheddar and parmesan cheese, combined with the squash gives this mac and cheese all the creaminess that would usually come from a base of butter, flour, and cream.
  • Veggie-packed. If you share your home with picky eaters, I urge you to give this butternut mac and cheese a try. Between the tender pasta and the thick, tasty sauce, you’d never guess that this version is packed with vegetables.

We love pasta casseroles in my family, and this baked butternut macaroni and cheese is right up there with both my best-ever lasagna recipe and its gluten free version as an all-time favorite!

Butternut squash macaroni and cheese is spooned out of a baking dish

What You’ll Need

This creamy butternut mac and cheese is one of the BEST ways to sneak in extra veggies for picky eaters (of all ages)! Here’s the short list of what you’ll need to make it. Scroll to the recipe card for a printable ingredients list.

  • Dry Pasta – I use quinoa pasta, butyou can use any gluten free or regular pasta. Any shape of pasta works in this butternut squash macaroni and cheese recipe. I just think mac and cheese is classic with elbow macaroni!
  • Butternut Squash – You’ll need a good sized squash peeled and cut into large chunks. See my tips for safely cutting up butternut squash below.
  • Broth – Either chicken or vegetable broth or stock.
  • Milk – I’ve used both 1% and 2% milk in this recipe, both with great results. Feel free to swap regular milk with your choice of dairy-free alternative, if needed.
  • Dry Mustard Powder – Some say it’s optional, but a touch of mustard is the secret to more flavor in any mac and cheese recipe! The tanginess makes the sauce taste cheesier, even without extra cheese.
  • Frozen Peas – Also optional. Tossing in a handful of peas adds color, and it’s my way of hiding even more vegetables in plain sight. If your picky eaters have eagle-eyes, feel free to skip the peas.
  • Sharp Cheddar Cheese and Parmesan Cheese – You’ll want to grate the cheese fresh from the block, rather than buying packaged shredded cheese. Freshly grated cheese melts down more smoothly.
  • Butter, Salt and Pepper – You can use unsalted or salted butter, whichever you have on hand.
A close up of butternut squash mac and cheese.

How to Peel and Cut Butternut Squash

Before you make your butternut mac and cheese, you’ll need to cut up the squash. You’ll need a sharp knife, or a vegetable peeler. Then, follow these quick steps:

  • If you’re using a peeler, chop off the top and bottom ends of the squash, and then use the peeler to remove the skin lengthwise. Afterward, chop the peeled squash into large chunks.
  • If you’re using a knife, it’s better to halve the squash horizontally, then place the squash ends cut-side-down and use the knife to slice off the peel before cutting it into chunks.
  • You can also soften the squash to make it easier to peel. To do so, poke holes in the skin using a fork and then microwave it for a couple of minutes before following the instructions above.

How to Make Butternut Squash Mac and Cheese

Once you’ve gathered your ingredients and chopped up your butternut squash, the rest of the recipe comes together in no time. Here are the steps involved. Scroll down to the recipe card for printable recipe instructions.

  • Cook the butternut squash. I usually steam the butternut squash like I do for my butternut squash casserole. You can also roast butternut squash in the oven or in the air fryer. Choose your preferred method.
  • Cook the pasta. Meanwhile, boil your choice of pasta al dente (firm, with a little bite) according to the package directions. 
  • Make the sauce. Blend the cooked butternut squash with the broth in a blender or food processor. Add the puree to a large pan on the stovetop with milk and butter, and bring it to a low boil.
  • Add the cheese. Next, add the mustard powder, cheddar cheese, and about 3/4 of the parmesan cheese, stirring as the cheese melts into the sauce.
  • Combine. Stir in the frozen peas, season the sauce to taste, and then fold in the pasta. Transfer everything to a baking dish. Give the top a sprinkle with leftover parmesan.
  • Bake. Finally, bake the mac and cheese at 350ºF for 20-25 minutes, until the cheese is hot and bubbly and the top is golden brown. Let the dish rest a bit once it’s out of the oven, and then serve!
Butternut mac and cheese in a baking dish.

Recipe Tips and Variations

Ask any home chef: most have secrets they swear by when making perfect macaroni and cheese. This recipe is no different! Here are my tips, plus some tasty add-in ideas for this butternut squash macaroni and cheese:

  • Season the pasta water. As a good rule of thumb, add 2-3 generous spoonfuls of table salt to the water you use to boil the pasta. The water must taste “salty like the Mediterranean” for well-seasoned, tastier noodles (I’m paraphrasing the Italians, but you get it!).
  • Change up the flavors. You can easily make this recipe more “adult” by swapping out the mustard powder for dijon mustard, adding in chili powder, or mixing in garlic for bolder flavors.
  • Add more protein. Bulk up this casserole with extra proteins like ground beef, sausage, or make a butternut squash-filled bacon and chicken mac and cheese.
  • More veggies. Mix in finely chopped carrots or broccoli, mixed frozen vegetables, sauteed or roasted mushrooms, or cherry tomatoes for even more veggie goodness in every bite.
  • Add herbs. Garnish this butternut squash mac and cheese with fresh parsley or basil.
A bowl of butternut squash macaroni and cheese

Make It a Meal

Butternut mac and cheese is delicious as an entree or as a side dish. Serve this next to easy roast chicken or air fryer chicken for weeknight meals. We love a side of honey roasted carrots or this easy lemon parmesan roasted broccoli. Both are easy to make while the oven is hot! This butternut macaroni and cheese also makes a great pairing with a crunchy Italian wedge salad, this easy Greek salad, or a plate of chef’s salad lettuce wraps.

Butternut squash macaroni and cheese served in a bowl with a blue and white fork.

How to Store and Reheat Leftovers

  • Refrigerate. You can keep and enjoy any leftover butternut squash mac and cheese for 3-5 days if stored airtight and in the fridge.
  • Reheat. To keep this mac and cheese moist on the reheat, sprinkle it with a spoonful of milk and cover it in foil before reheating it in the oven. You can also reheat it in the microwave covered in plastic wrap (poke holes in the top for steam to escape).

Can I Freeze Butternut Squash Mac and Cheese?

Yes! This butternut squash macaroni and cheese freezes well, either whole or in portions, for easy reheating. Wrap the cooled casserole in a layer of plastic wrap, plus a layer of aluminum foil to prevent freezer burn. Freeze the mac and cheese for up to 3 months. Defrost in the fridge before reheating.

Full disclaimer: If you make this recipe with gluten free pasta, it will get a bit mushy from freezing and thawing. That’s just the nature of these types of noodles. But your mac and cheese will still taste delicious!

More Gluten Free Pasta Recipes

Butternut squash macaroni and cheese is spooned out of a baking dish
5 from 6 votes

Butternut Squash Mac and Cheese

This Butternut Squash Mac and Cheese has all the creamy flavors of classic macaroni and cheese, wrapped up in a kid-friendly, gluten free pasta recipe with added veggie power.
Prep: 20 minutes
Cook: 40 minutes
Total: 1 hour
Servings: 6 servings

Ingredients

  • 1 medium butternut squash peeled and cut into large chunks
  • 8 oz dry quinoa pasta or other gluten free-pasta, or half of a 1 lb. box of regular pasta
  • 3 Tablespoons chicken or vegetable broth
  • 1 cup milk I’ve used 1% and 2%
  • 1 Tablespoon butter
  • 1 teaspoon dry mustard
  • 1 1/2 cups sharp cheddar cheese
  • 1/2 cup parmesan cheese divided
  • 1/2 cup frozen peas
  • salt and pepper to taste

Instructions

  • Steam or microwave the butternut squash until it is soft and can be mashed easily, about 15 minutes.
  • Meanwhile, preheat your oven to 350°F. and cook the pasta according to package directions, leaving it slightly under cooked, or al dente.
  • In a blender or food processor, puree the butternut squash with the broth, adding enough so that it becomes a smooth puree.
  • In a large saucepan, combine the squash puree, milk and butter, and heat over medium heat until it just barely comes to a boil.
  • Add the dry mustard, cheddar cheese, and 1/4 cup of the parmesan cheese, and stir until the cheese is fully melted and incorporated.
  • Add the frozen peas, and salt and pepper, to taste.
  • Add the pasta to the cheese sauce, and stir to combine.
  • Pour the mixture into a glass or ceramic baking dish, and sprinkle the top with the remaining 1/4 cup parmesan cheese.
  • Bake for 20-25 minutes, or until hot and bubbly, and the top is slightly browned.
Nutrition Facts
Butternut Squash Mac and Cheese
Amount Per Serving (0.5 cup)
Calories 384 Calories from Fat 126
% Daily Value*
Fat 14g22%
Saturated Fat 9g45%
Cholesterol 43mg14%
Sodium 377mg16%
Potassium 565mg16%
Carbohydrates 49g16%
Fiber 3g12%
Sugar 5g6%
Protein 15g30%
Vitamin A 13825IU277%
Vitamin C 31.6mg38%
Calcium 413mg41%
Iron 1.3mg7%
* Percent Daily Values are based on a 2000 calorie diet.
Disclaimers: Please discuss your individual dietary needs (i.e. gluten free) with a physician. Even when not specified, be sure to verify all ingredients are gluten free, if needed, by reading labels on all packaging and/or confirming with the manufacturer this varies by brand and can change at any time. Nutrition information shown is an estimate and not guaranteed to be accurate.

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32 Comments
  1. Seema

    This looks great! Do you think I could make a batch & freeze some of it? Maybe put it in muffin tins & then freeze them afterwards? Thank you!!

    1. Brianne Cupcakes & Kale Chips

      Thank you, Seema! I think this recipe would freeze wonderfully! If you’re going to freeze it in muffin tins, I would suggest lining them with plastic wrap so that they pop out more easily. Once they’ve frozen, wrap them in the plastic wrap and store them in a freezer bag.

  2. Elizabeth

    5 stars
    I made this and it was AMAZING!!! I been on a squash kick and this was the perfect addition to my fall lineup! Absolutely amazing. My fiancé loved it 🙂 Thanks for this awesome share!!!

  3. Miriam

    -19 stars
    It does not say where to incorporate the squash puree in the directions. I just added after stirring the cheese and mac together. just wanted to let you know or maybe I missed something, either way it looks really good and my kids are about to try it. Thank you

  4. My son keeps BEGGING me to buy the blue box macs and cheese but I refuse to do it. Maybe this recipe will convert him away from that nasty processed stuff. Thanks for linking up at A Little Nosh!

  5. Alyssa

    I have never had butternut squash macaroni and cheese. This looks really good. I think this is a great recipe for kids, without them knowing they are eating really healthy. Thanks for sharing at Showcase Your Talent Thursday and I can’t wait to see what you have to share at the next party!

  6. 5 stars
    This is a beautiful dish and a meal in one, I look forward to making this delicious recipe! Hope you have a wonderful week and thank you so much for sharing with Full Plate Thursday.
    Come Back Soon!
    Miz Helen

  7. This looks delicious, I love how you made it healthier too. Now if only I can find quinoa pasta, I bet I would love it. thanks for sharing on Newlyweds recipe linky, I pinned this recipe too!

  8. I’ve had quinoa pasta before and I really like it – just wish it wasn’t so expensive by me. 🙁

    Your dish looks delicious!!

  9. Tastefully Julie

    I made a Martha Stewart recipe once for butternut squash mac and cheese. It was so good! The kids loved it until I told them it had squash in it. Now every single night, no matter what I make, they say “Is there squash in this?”.

  10. And a glass of red wine

    WOW! the pictures are so amazing! Glad the Bug loved it! Love how you added color to it! Might need to do that with some broccoli on my end! Thanks for the tag!

  11. I’ve been mac & cheese obsessed the past 2 days! Except mine didn’t look as good as this! Mine was kraft Sponge Bob Mac & Cheese in a cup! lol But I did add a slice of pepper jack and a minced sun-dried tomato to give it some flare!
    Great post!

5 from 6 votes (2 ratings without comment)

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