This Butternut Squash Macaroni and Cheese is so creamy and comforting with healthy squash that’s made on the stovetop!

butternut squash mac and cheese in a bowl

I love butternut squash recipes at the end of fall as we head into winter; it’s the perfect squash for so many seasonal recipes. If you love this stovetop mac and cheese recipe, try our Butternut Squash Risotto, Butternut Squash Chili and Roasted Butternut Squash Soup next!

This one pot mac and cheese is one of those meals I love making on a Friday night and enjoying throughout the weekend.

If you’re planning on company or a holiday dinner, this butternut squash macaroni and cheese is perfect (and easy!) for the masses. Just prep a side salad beforehand and you’re good to go.

Or make this mac and cheese as a side to your Thanksgiving menu!

Butternut Squash Mac and Cheese

This mac and cheese is comforting and classic tasting but it’s loaded with nutrients (seriously, so many vitamins and fiber in a serving of butternut squash) so it’s on the healthier side as far as macaroni and cheese is concerned.

To make this Butternut Squash recipe you start with a very easy puree. And it’s all done on the stovetop – no need to turn on the oven or bake a thing! Easy peasy.

Ingredients in this recipe

Butternut Squash Puree

1 large butternut squash peeled, seeded, and cut into 1/2 inch cubes – or 1 (15-ounce bag) frozen cubed butternut squash (do not thaw)
1 1/2 cups water
1 1/2 tablespoons finely chopped sage – can also use dried spice
1 1/2 tablespoons fresh thyme sprigs – can also use dried spice
1 cup vegetable broth – or chicken broth
1 teaspoon Kosher salt
1 teaspoon pepper

Macaroni and Cheese

1 tablespoon ghee – or butter
1 tablespoon tapioca starch – can also use arrowroot, cornstarch or flour
3 cloves garlic, minced
1 1/2 cups almond milk – any milk is fine
1 tablespoon Dijon mustard
1-lb macaroni of choice, cooked to package directions – can also use rigatoni or penne pasta
1 1/2 cups grated sharp cheddar cheese – about 6 ounces
1/4 cup finely grated Parmesan cheese – plus more for garnish

I recommend using block cheddar cheese and shredding with a grater. There are preservatives in already shredded cheese that do not melt the same way as blocked cheddar cheese.

The pasta will continue to cook a bit once you add to the butternut squash puree. To avoid overcooking, make sure to cook your macaroni pasta al dente (still firm when bitten).

Butternut Squash Puree

The creamy butternut squash puree that we’ll mix together with our Parmesan and Cheddar Cheese Sauce is the perfect way to enjoy more veggies without thinking much about it.

You can cube fresh squash if it is in season or use frozen in a pinch – I have made this dish both ways and it’s delicious every time. You can either cube and peel fresh squash or use a bag of frozen squash. Both come together in the blender with broth and spices, before stirring into this mac and cheese recipe.

And if you’re really pressed for time the day of, remember that this puree can also be made in advance and stirred in right before serving.

vegetarian option

There are so many delicious and creative ways to make a Butternut Squash Mac and Cheese that is vegan, but this one isn’t it. We call for Cheddar and Parmesan cheeses for this macaroni.

But to keep it vegetarian, make sure to use vegetable broth for the puree.

tools you’ll need for butternut squash mac and cheese

large saucepan or stockpot
chef’s knife
cutting board
blender
cheese grater
whisk
colander

HOW TO STORE

To Store. Refrigerate leftover Butternut Squash Mac + Cheese in an airtight storage container for up to 4 days.
To Reheat. Warm leftovers on the stovetop in a saucepan over medium-low heat or in the microwave.
To Freeze. Freeze mac and cheese in an airtight freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before reheating.