Steamed and pureed butternut squash is the foundation for this velvety cheese sauce. Need butternut squash mac and cheese for toddlers (or those with toddler palates?). Because butternut squash is mild and sweet, picky eaters will never suspect it’s loaded with veggies (mwahaha!).

Like my Pumpkin Mac and Cheese and Instant Pot Cauliflower Mac and Cheese, this easy butternut squash mac and cheese tastes much more indulgent than it is, thanks to healthy swaps like Greek yogurt and whole wheat pasta in place of white.I did make this butternut squash mac and cheese with bacon and breadcrumbs (because, tasty!), but you can leave these out if you prefer to keep things as lean as possible.

This healthy butternut squash mac and cheese is also make-ahead friendly. Keep this recipe in mind for make-ahead dinners and future holidays. I have all the storage and meal-prep tips you need below.

How to Make Butternut Squash Mac and Cheese

To make this tasty butternut squash macaroni and cheese as quick and easy as possible, I used frozen, steam-in-the-bag cubed butternut squash. You can swap fresh or roasted too. We paired this butternut squash recipe with Slow Cooker Pulled Pork, but it can easily be a stellar stand-alone dish, perhaps with an Apple Walnut Salad, or coupled with a more elegant entrée like Crockpot Pork Roast or Bacon Wrapped Chicken Breast.

The Ingredients

Whole Wheat Pasta. An instant way to bump up the nutritional value of any pasta recipe.

Butternut Squash. Adds sweet, nutty deliciousness to our scrumptious sauce without detracting from the cheesy flavor. Plus, butternut squash is rich in antioxidants, vitamins, and fiber.

Bacon or Pancetta. Hello, crowd-pleasing, MVP addition! The drippings add a wonderful savoriness to the sauce. Nonfat Milk. Helps make the sauce creamy. Dry Mustard. Accentuates the cheesy flavors without being overpowering. Spices. Nutmeg is a classic in creamy sauces and provides nuttiness; cayenne gives just a hint of spice. The spices bring out the flavor of butternut squash.Cheeses. Parmesan and sharp cheddar are the ideal cheeses for this butternut squash mac and cheese. The Parmesan acts as a salty complement and the sharp cheddar makes this recipe as all-American as, well, macaroni and cheese!

Greek Yogurt. Makes the sauce extra creamy and slightly tangy, just like in my classic Instant Pot Mac and Cheese. Make sure to use full-fat Greek yogurt so it doesn’t curdle. Parmesan Breadcrumb Topping. Cheesy and crispy. Need I say more?

The Directions

Storage Tips

To Store. Refrigerate mac and cheese in an airtight container for up to 3 days. To Reheat. Rewarm leftovers in a baking dish in the oven at 350 degrees F 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.

If we can turn a healthy, nutrient-dense vegetable into a creamy pan of mac and cheese bliss, is there anything we can’t do? For a more robust, caramelized squash flavor, make roasted butternut squash mac and cheese.

See my Roasted Butternut Squash for tips on cutting butternut squash and how to roast it (omit the cinnamon if using for mac and cheese).

Pre-shredded cheeses are coated with a starchy substance meant to reduce clumping. That substance will cause your cheese not to melt as smoothly.Off-the-block cheese is usually less expensive than pre-shredded too.

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