Butternut Squash Macaroni and Cheese

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

I began making this recipe when my son entered preschool. He’s always ate 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!

• 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!

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 because it’s gluten free but sturdier for baked pasta casseroles. But you can use any gluten free or regular pasta. Any shape of pasta works in this butternut squash macaroni and cheese recipe. Elbow macaroni is classic, but the quinoa pasta I like is more readily available as penne.
• 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.
• Butter – You can use unsalted or salted butter, whichever you have on hand.
• 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.
• Sharp Cheddar 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. You can use white or yellow cheddar – it doesn’t affent the flavor, just the color.
• Parmesan Cheese – Shredded or grated will both work though I prefer grated. Some parm gets mixed into the sauce and some is sprinkled on top for a nice, golden finish.
• Frozen Peas – 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.
• Salt and Pepper – Season to taste.

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.

• Prep the casserole. 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!

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!).
• Use the right GF pasta. Some types of gluten free pasta don’t hold up well to boiling then baking. I like to use quinoa pasta like the Banza brand when I am making a pasta casserole like baked mac and cheese. If you cook it al dente, it won’t dinstegrate when you combine it with the sauce and bake 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.

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!