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Sneaking vegetables into creamy, decadent-tasting pasta sauces is a delicious bit of magic, especially when it’s this Butternut Squash Mac and Cheese! Whether you’re looking to appease picky toddlers or simply want a healthy version of a comfort pasta classic, this is the recipe for you.

Butternut squash mac and cheese recipe with breadcrumb topping

Why You’ll Love This Healthy Butternut Squash Mac n’ Cheese Recipe

  • Nutritious Comfort Food. Pureed butternut squash is the foundation for the velvety cheese sauce. However (like my Pumpkin Mac and Cheese), this easy butternut squash mac and cheese tastes much more indulgent than it is. Healthy swaps like Greek yogurt and whole wheat pasta make it wholesome without sacrificing flavor or texture.
  • Fancy if You Like. 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.
  • Great for Kids and Adults. Because butternut squash is mild and sweet, picky eaters will never suspect this pasta is loaded with veggies Cauliflower Mac and Cheese, and Butternut Squash Pasta). This recipe looks elegant and tastes elevated without losing its inherent kid-friendly, cheesy appeal.
  • Easy Shortcuts. Thanks to frozen butternut squash, this comes together quickly. Just steam in the bag and blend.
  • Serve it for a Side Dish or Main Dish. 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.
Easy Butternut squash mac and cheese on a plate next to salad

How to Make Butternut Squash Mac n’ Cheese

The Ingredients

  • Whole Wheat Pasta. An instant way to bump up the nutritional value of any pasta recipe. I recommend using a high-quality whole-wheat pasta for the ideal texture.
  • 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

  1. Steam the Squash. Transfer it to a blender. Cook the pasta. Prep the topping.
Bacon in a skillet
  1. Cook the Bacon. Sauté the shallot in the bacon drippings.
Butternut squash puree in a blender
  1. Puree the Squash. Pour the milk and broth into the blender, blending until smooth. Pour the mixture into the pot and add the other spices.
Cheese sauce in a pot next to a bag of pasta
  1. Simmer. It will become thick and luscious.
Sauce ingredients being stirred in a pot
  1. Make the Sauce. Whisk in the cheese and yogurt.
Pasta with a cheesy sauce in a pot
  1. Stir. Add the noodles and bacon.
A photo showing how to make healthy  mac and cheese with butternut squash
  1. Assemble the Mac and Cheese. Scatter the breadcrumb topping mixture over the top.
Butternut squash mac and cheese with bacon
  1. Bake. 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!
frozen Butternut squash mac and cheese on a plate

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.

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).

healthy butternut squash mac and cheese in a baking dish

What to Serve With Butternut Squash Mac and Cheese

Healthy butternut squash mac and cheese in a baking dish
  • Baking Dish. I love this baking dish, and it’s dishwasher-safe.
  • Cheese Grater. A must-have tool for grating your own cheese.
  • Dutch Oven. An all-purpose kitchen tool that you’ll have for a lifetime.
A plate with butternut squash mac and cheese

Recipe Tips and Tricks

  • Grate Your Own 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.
  • Use Full-Fat Yogurt. Using full-fat yogurt is important here. A yogurt with less fat content is very likely to curdle.
  • Roasted Squash Upgrade. For a more robust, caramelized squash flavor, make roasted butternut squash mac and cheese (steamed squash works well too). 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).

Butternut Squash Mac and Cheese

4.86 from 7 votes
This easy butternut squash mac and cheese sneaks butternut squash into the sauce for a healthy twist. Great for toddlers and picky eaters!

Prep: 10 minutes
Cook: 55 minutes
Total: 1 hour 5 minutes

Servings: 10 servings


  • 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 whole wheat pasta use any chunky shape, such as cavatappi (pictured), 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°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 to 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 and broth 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 least 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°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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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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    1. Hi Nancy! Thanks so much for letting me know! You add it with the milk! I’ve updated it in the recipe card! Thanks again! Hope you enjoy it!

  1. I’d make this again — its so much more healthier compared to my delish mac n cheese that’ll make the south so darn proud. This one is something I can make without trailing far off my goal to eat healthier and better. My boyfriend even loves it!5 stars

  2. Hi Erin,

    Would I be able to make this casserole up to step 11 about 2-3 hours in advance and store in the fridge before placing in the oven? Thanks!

    1. Hi Selena! My initial thought would be yes the only problem you may run into is that your creamy sauce will thicken up in the refrigerator, which would require you to bake it longer. If you decide to experiment, let me know how it goes!

  3. This was so delicious. Hard to stop eating it! Best butternut squash mac and cheese we have made. Lots going on when making the recipe, but worth every step!5 stars

  4. Hi Erin, if I’m making this with fresh squash is it ok to roast the cubes in the oven rather than boiling? Thanks!

  5. This was incredibly good and incredibly easy! I steamed my fresh squash in the microwave and added more bacon than called for, otherwise I followed the recipe. It was delicious on the day and delicious all week long as leftovers I took for lunch. I will definitely be making this again.5 stars

  6. This was incredible! What a perfect way to use up a butternut squash I had on my counter. Since it was a fresh one, I split it in half and pressure cooked it before scooping out the flesh and proceeding with the recipe. Other than that, followed it exactly and it came out amazing. Decadent yet healthy. Thank you!5 stars