Butternut Squash Mac and Cheese {Easy and Healthy} – WellPlated.com


Sneaking vegetables into creamy, decadent-tasting pasta sauces makes me feel oddly powerful. The latest bit of magic: Butternut Squash Mac & Cheese!

Butternut squash mac and cheese with breadcrumb topping

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This recipe is sponsored by DeLallo.

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 (mwahaha!).

  • Like my Pumpkin Mac and Cheese and Instant Pot Cauliflower Mac and Cheese, the cheesy sauce 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.
Butternut squash mac and cheese on a plate next to salad

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.

Healthy butternut squash mac and cheese in a baking dish

How to Make Butternut Squash Mac and Cheese

To make this 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.

A plate with butternut squash mac and cheese

The Ingredients

  • Whole Wheat Pasta. An instant way to bump up the nutritional value of any pasta recipe. If you’ve found whole wheat pasta dry or chewy in the past, it is likely the brand you selected. I use and recommend DeLallo. The texture is spot-on and the taste mild. Everyone will think it’s regular pasta!

Fun Shapes!

In addition to having a superior taste and texture, I also love that DeLallo whole wheat pastas come in so many fun shapes.

For the butternut squash mac and cheese, I used the whole wheat cavatappi. I love the way the thick, twirly noodles twine around the sauce.

Butternut squash mac and cheese with bacon
  • 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.

Using Fresh or Roasted Butternut Squash

You can steam fresh butternut squash cubes and use them in place of the frozen cubes.

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).
  • Bacon or Pancetta. Hello, crowd-pleasing, MVP addition! The drippings add a wonderful savoriness to the sauce that takes it to the next level.
  • 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.
  • 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!

Tip!

Rather than purchasing already shredded cheese in a bag, grate it yourself right off the block.

  • 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.
  • Greek Yogurt. Makes the sauce extra creamy and slightly tangy. 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

  1. Steam and drain the squash. Transfer it to a blender. Cook the pasta and stir together the topping.
Bacon in a skillet
  1. Cook the bacon. Remove it to a paper towel-lined plate. Sauté the shallot in the bacon drippings.
Butternut squash puree in a blender
  1. Pour the milk into the blender. Blend until smooth, then pour the mixture into the pot and add the other spices.
Cheese sauce in a pot next to a bag of pasta
  1. Simmer the sauce to thicken.
Sauce ingredients being stirred in a pot
  1. Whisk in the cheeses and yogurt.
Pasta with a cheesy sauce in a pot
  1. Stir in the noodles and bacon.
Butternut squash mac and cheese in a baking dish
  1. Transfer the mac and cheese to a baking dish, and scatter the breadcrumb topping mixture over the top.
  2. Bake butternut squash mac and cheese at 400 degrees F for 25 minutes. Broil for 2 to 3 minutes. Top with fresh chives and ENJOY!
Butternut squash mac and cheese on a plate

Wine Pairing

Serve butternut squash mac and cheese with Chardonnay or Riesling. If you prefer reds, try a fruity Pinot Noir or Malbec.

Storage Tips

  • To Store. Refrigerate mac and cheese in an airtight storage 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.
Creamy butternut squash mac and cheese in a baking dish

Meal Prep Tip

Up to 1 day in advance, steam the squash cubes, cut the bacon or pancetta, chop the shallot, and grate the cheeses. Refrigerate each ingredient in a separate airtight storage container.

Leftover Ideas

Bulk up your mac and cheese leftovers by stirring in some Crock Pot Shredded Chicken or ground meat (turkey or beef would be tasty).

What to Pair with Butternut Squash Mac and Cheese

Butternut squash’s lightly sweet, caramelized flavor makes it ideal for pairing with a wide range of proteins, including chicken, pork, and beef. It also works well in hearty vegetarian mains.

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Butternut squash mac and cheese with breadcrumb topping

Did you make this recipe?

Let me know what you thought!

Leave a rating below in the comments and let me know how you liked the recipe.

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?

Exercise your pasta powers tonight!

Frequently Asked Questions

How Can I Make Vegetarian Butternut Squash Mac and Cheese?

To make vegetarian butternut squash mac and cheese, simply omit the bacon. Sauté the shallot in 1/2 tablespoon of olive oil instead of the bacon drippings.

Can I Omit the Cayenne?

While this mac and cheese recipe is not spicy, if you need it to be completely spice-free, you can omit the cayenne pepper.

Can I Use a Different Type of Milk?

Yes, you can use any unflavored milk you have on hand. I used nonfat milk to keep things light, but any dairy milk, soy milk, or almond milk will work fine.

  • 1 pound frozen cubed butternut squash or fresh squash cut into 3/4-inch cubes, about 1 small squash
  • 4 strips bacon or pancetta* cut into bite-sized pieces, optional
  • 1/4 cup finely chopped shallot or yellow onion
  • 1 cup nonfat milk
  • 1 cup low-sodium chicken broth or vegetable broth
  • 16 ounces DeLallo Cavatappi Whole Wheat Pasta or any chunky shape, such as rigatoni or penne
  • 1 teaspoon dry mustard
  • 3/4 teaspoon kosher salt
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon cayenne pepper
  • 1 cup freshly shredded sharp cheddar cheese about 4 ounces
  • 1/4 cup grated Parmesan cheese about 3/4 ounce
  • 2/3 cup whole plain Greek yogurt do not use low fat or fat free or it may curdle
  • Chopped fresh chives optional, for serving

FOR THE TOPPING:

  • 1/4 cup grated Parmesan cheese about 3/4 ounce
  • 1/4 cup Panko breadcrumbs
  • 1 1/2 teaspoons extra-virgin olive oil

  • Preheat the oven to 400 degrees F. Coat a 9×13-inch baking dish with nonstick spray.

  • Steam the squash according to package instructions until fork tender (if cooking fresh squash, bring a large pot of water boil. Add squash and boil until tender, 4-6 minutes.). Drain the squash, then transfer to a blender.

  • Meanwhile, in a Dutch oven or similar deep, wide pot, cook the bacon over medium-low for 8 to 10 minutes, until the fat is rendered (don’t rush it or the bacon will burn). With a slotted spoon, transfer the bacon to a paper towel-lined plate and lightly pat dry. Discard all but 1/2 tablespoon drippings from the pot.

  • Return the pot to medium-low heat. Add the shallot and sauté until softened, about 5 minutes.

  • In a separate pot, cook the pasta until nearly al dente. It shouldn’t be completely crunchy but when you taste it, it should still be too firm to eat. Drain and set aside.

  • In a small bowl, stir together the topping ingredients: Parmesan, panko, and olive oil. Set aside.

  • Add the milk to the blender with the squash. Blend until smooth, then pour into the pot with the shallot. Add the mustard, salt, nutmeg, and cayenne. Stir until combined.

  • Bring the sauce to a gentle boil. Reduce the heat as needed to maintain a steady simmer. Simmer, stirring very often to prevent sticking, until the sauce is thickened, about 5 minutes. Remove from the heat and let cool 3 minutes.

  • Whisk in the cheddar, Parmesan, and Greek yogurt until smooth. Taste and add additional seasoning as desired.

  • Gently stir the noodles and bacon into the sauce.

  • Scoop into the prepared baking dish (it will seem very saucy). Sprinkle the topping mixture over the top.

  • Bake the butternut squash mac and cheese for 25 minutes, then turn the oven to broil. Broil for 2 to 3 minutes until the Panko is lightly browned. DO NOT walk away or the topping may burn when you let expect it. Sprinkle with fresh chives. Let cool a few minutes, then enjoy hot.

  • *For a vegetarian butternut squash mac and cheese, omit the bacon. Sauté the shallot in 1/2 tablespoon olive oil instead of the bacon drippings.
  • Adapted from my Pumpkin Mac & Cheese.
  • TO STORE: Refrigerate mac and cheese in an airtight storage 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. 

Serving: 1(of 10)Calories: 312kcalCarbohydrates: 38gProtein: 15gFat: 11gSaturated Fat: 5gPolyunsaturated Fat: 1gMonounsaturated Fat: 4gTrans Fat: 1gCholesterol: 23mgPotassium: 297mgFiber: 4gSugar: 4gVitamin A: 5043IUVitamin C: 10mgCalcium: 210mgIron: 1mg

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I am sharing this post in partnership with DeLallo. As always, all opinions are my own. Thanks for supporting the brands and companies that make it possible for me to continue to create quality content for you!

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