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This healthy butternut squash mac and cheese is seriously so good! It’s creamy, cheesy, and packed with cozy fall flavor, but made lighter without heavy cream, butter, or oil. The butternut squash adds so much flavor and gives this mac and cheese its creamy texture and natural sweetness.

Healthy Butternut Squash Mac and Cheese in a bowl.

Ella and I make this all the time, and she always jokes that while it officially serves four, it really only serves one when she’s around! We both love how creamy and cheesy it is! Whether you’re making it for a cozy family dinner, a holiday side dish, or just want a comforting fall meal, this is one you’ll want to make on repeat! For more delicious mac and cheese recipes, try our cottage cheese mac and cheese, healthy mac and cheese with tofu, and pumpkin mac and cheese next!

🔎 Quick Look: Healthy Butternut Squash Mac and Cheese

  • ⏱️ Prep Time: 20 minutes
  • ⏱️ Cook Time: 10 minutes
  • 🕒 Total Time: 30 minutes
  • 🍽 Calories: ~173 kcal per serving
  • 👥 Servings: 4
  • 🥣 Key Ingredients: Butternut squash, elbow macaroni, cheddar cheese powder, shredded light cheddar cheese, Parmesan cheese, milk, seasonings
  • 👩‍🍳 Cook Method: Boil butternut squash, and heat the sauce in a saucepan on the stovetop
  • ⭐ Difficulty: Easy

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Why You Will Love This Recipe

  • Better Than Trader Joe’s: If you love Trader Joe’s butternut squash mac and cheese, you’ll love this homemade version even more! It’s creamier, fresher, and packed with flavor.
  • Healthy: It’s such a classic fall favorite that we have lightened up! There’s no heavy cream, half-and-half, butter, or oil in this recipe!
  • Easy to Make: This recipe comes together quickly in about 30 minutes for an easy and delicious meal!
  • Creamy Texture: This mac and cheese is incredibly decadent and creamy.
  • Delicious Flavor: It’s the perfect balance of flavors between the butternut squash, cheese, and cozy spices. This recipe is truly incredible!

Key Ingredients

Ingredients for butternut squash mac and cheese in bowls.
  • Elbow Macaroni: Use elbow macaroni or your pasta of choice for this recipe.
  • Butternut Squash: You will need one pound of peeled and chopped butternut squash. To save time, you can buy a package already done to use in this recipe. For more butternut squash recipes, try our air fryer butternut squash and butternut squash apple soup next!
  • Cheddar Cheese Powder: The cheddar cheese powder adds an incredible cheesy flavor without needing as much shredded cheese. It makes this recipe lighter while still delivering a classic cheesy flavor.
  • Shredded Cheddar Cheese: In addition to the cheddar cheese powder, add light shredded cheddar cheese.
  • Parmesan: Grated Parmesan cheese adds another layer of cheesy goodness.
  • Milk: Use your milk of choice. The milk helps make this sauce the ideal consistency.
  • Mustard: A touch of stone-ground mustard adds incredible depth of flavor its our favorite to use. If you don’t have stone-ground mustard, use Dijon.

Find the full list of ingredients and measurements in the recipe card below.

Substitutions & Variations

  • Pasta Options: Feel free to use your favorite pasta shape or a pasta alternative for this recipe! For a lighter twist, use zucchini noodles, hearts of palm Palmini pasta, or spaghetti squash noodles. Or, for a low-carb alternative, use Carba-Nada pasta or Fiber Gourmet pasta. We even love using protein pasta, such as Brami or Kaizen for a boost of protein and fiber.
  • Roast The Butternut Squash: You can roast your cubed butternut squash instead of boiling it! Toss the cubes with a little olive oil, salt, and pepper, and roast at 400°F for about 25-30 minutes, until tender and caramelized. Then, blend the roasted squash into the cheese sauce. Roasting the sauce adds even more sweetness and depth of flavor.
  • Canned Butternut Squash Puree: You can substitute the cubed butternut squash with one can of fresh butternut squash puree! This speeds up the process and adds a rich, creamy texture to the sauce. You could even use a can of pumpkin puree for this recipe or make our pumpkin mac and cheese! Or, try our pumpkin pasta sauce.
  • Baked Version: You can bake this butternut squash mac and cheese instead of heating it up on the stovetop. Mix the cooked pasta with the sauce and transfer it to a baking dish. Then, bake it at 350°F for 10-15 minutes, or until done. 
  • Add Breadcrumbs: For a crunchy topping, sprinkle with regular breadcrumbs or Panko breadcrumbs before baking.
  • Cheese Options: You can experiment with different types of cheese to personalize your mac and cheese! You could substitute the light shredded cheddar cheese for shredded Gruyere. Or, swap the Parmesan cheese for crumbled feta cheese for a different flavor profile! Any of these cheese options complement the flavors of the butternut squash!

How to Make Healthy Butternut Squash Mac and Cheese

Drained boiled butternut squash in a strainer.
  1. Boil the peeled and chopped butternut squash in a large pot of salted boiling water on the stovetop for 10-12 minutes. Once done, drain the butternut squash and let it slightly cool.
Drained and cooked elbow macaroni.
  1. Cook the elbow macaroni or your pasta of choice according to the package directions. Once the pasta is cooked, drain it and set it aside.
Blended butternut squash mac and cheese sauce in a blender.
  1. Add the boiled and drained butternut squash to a blender. Next, add the cheddar cheese powder, light shredded cheddar cheese, grated Parmesan cheese, milk, mustard, garlic powder, onion powder, salt, pepper, smoked paprika, nutmeg, and cinnamon to the blender. Then, blend the sauce until smooth.
Combined sauce with macaroni in a saucepan.
  1. Heat the blended sauce in a saucepan over low heat until warm. After that, add the cooked and drained pasta, stirring until it is fully coated in the sauce.

Expert Tips

  • Blend the Sauce: Thoroughly blend the sauce until it is smooth and creamy to incorporate all the ingredients.
  • Buy Chopped Butternut Squash: You can buy butternut squash already peeled and cubed to make it easier and quicker.
  • Grate the Cheese: You can buy pre-grated cheese to save time or grate the cheddar and Parmesan cheese yourself for an even richer flavor.
  • Protein Boost: You can mix in a fully cooked protein such as shredded chicken, chopped sausage, or bacon bits. To boost the protein even more, use protein pasta in this recipe.

Serving Suggestions

We love serving this butternut squash mac and cheese with side dishes such as air fryer frozen broccoli, roasted Brussels sprouts, or crispy green beans. Or, serve it with a salad, such as our shaved Brussels sprout salad! It also makes a great addition to a holiday spread!

Storage Instructions

Store leftovers in an airtight container in the refrigerator for up to 3 days. Reheat it in the microwave or in a saucepan on the stovetop with a splash of milk to maintain its creaminess.

Butternut Squash Mac and Cheese FAQs

What Does Butternut Squash Mac and Cheese Taste Like?

This butternut squash mac and cheese has a rich and creamy texture reminiscent of classic mac and cheese. It’s enhanced by the earthy depth of flavor and natural sweetness of butternut squash! The butternut squash complements the cheesy goodness, creating a comforting and satisfying dish!

Can You Freeze Butternut Squash Mac and Cheese?

Yes, you can freeze this homemade butternut squash mac and cheese! Store it in a freezer-safe container and freeze it for 2-3 months. When ready to serve it again, thaw it in the refrigerator overnight and then bake it in an oven-safe dish at 350°F for about 20 minutes, or until fully warmed through.

More Recipes to Try Next!

If you try this recipe please be sure to leave us a comment and star rating, ★★★★★, letting us know how it turns out for you.

5 from 2 votes

Healthy Butternut Squash Mac and Cheese

Prep: 20 minutes
Cook: 10 minutes
Total: 30 minutes
Servings: 4 servings
This healthy butternut squash mac and cheese is incredible! It’s a lighter version that’s cheesy, creamy, delicious, and perfectly balanced with cozy fall flavors.
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Ingredients 

  • 10 ounces dried elbow macaroni
  • 1 pound butternut squash, peeled and chopped
  • 1/4 cup cheddar cheese powder
  • 3 ounces shredded light cheddar cheese
  • 2 tablespoons grated Parmesan cheese
  • 1/4 cup milk of choice
  • 1/2 teaspoon stone-ground mustard or Dijon
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 1/2 teaspoon salt
  • 1/4 teaspoon black pepper
  • 1/4 teaspoon smoked paprika
  • 1/4 teaspoon ground nutmeg
  • 1/8 teaspoon ground cinnamon

Instructions 

  • Boil the peeled and chopped butternut squash in a large pot of salted boiling water on the stovetop for 10-12 minutes, or until fork-tender. Once done, drain the butternut squash and let it slightly cool.
  • Cook the elbow macaroni or your pasta of choice according to the package directions. Once the pasta is cooked, drain it and set it aside.
  • Add the boiled and drained butternut squash to a blender. Next, add the cheddar cheese powder, light shredded cheddar cheese, grated Parmesan cheese, milk, mustard, garlic powder, onion powder, salt, pepper, smoked paprika, nutmeg, and cinnamon to the blender. Then, blend the sauce until smooth and creamy.
  • Heat the blended sauce in a saucepan over low heat until warm. Once warm, add the cooked and drained pasta, stirring until it is fully coated in the sauce.

Video

Notes

  • Pasta to Use: Feel free to use your favorite pasta shape or a pasta alternative for this recipe! To evoke the nostalgia of classic mac and cheese, we recommend elbow macaroni. For a lighter twist, use zucchini noodles, hearts of palm, or spaghetti squash noodles. Or, for a low-carb alternative, use Carba Nada pasta or Fiber Gourmet pasta. To boost the protein, use protein pasta such as Brami or Kaizen.
  • Chopped Butternut Squash: You can buy butternut squash already peeled and cubed to make it easier and quicker.
  • Protein Boost: You can mix in a fully cooked protein such as shredded chicken, chopped sausage, or bacon bits.
  • Roast the Butternut Squash: You can roast your cubed butternut squash instead of boiling it! Toss the cubes with a little olive oil, salt, and pepper, and roast at 400°F for about 25-30 minutes, until tender and caramelized. Then, blend the roasted squash into the cheese sauce. Roasting the sauce adds even more sweetness and depth of flavor.
  • Storage: Store leftovers of this butternut squash mac and cheese in an airtight container in the refrigerator for up to 3 days.
 
WW Points: 8 points per serving
To see your WW Points in the WW app for this recipe click here! Or, please manually add the ingredients to the recipe builder.

Nutrition

Calories: 173kcal, Carbohydrates: 38.6g, Protein: 8.4g, Fat: 4g, Saturated Fat: 1.8g, Cholesterol: 9mg, Sodium: 680mg, Fiber: 12.5g, Sugar: 4.2g

Nutrition information is automatically calculated, so should only be used as an approximation.

Tried this recipe?Mention @wwhealthyfoodiegirl or tag #healthyfoodiegirl!
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About Us

Welcome to Healthy Foodie Girl! We’re Shawna and Ella, a mother-daughter team. We create healthy, flavorful recipes featuring high-protein meals, Weight Watchers-friendly recipes, and lighter versions of your favorite dishes.

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5 from 2 votes

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Recipe Rating




3 Comments

  1. Alex says:

    5 stars
    Oh my God! Who doesn’t like macaroni and cheese? This is a fantastic recipe and it’s always a hit with the family. I love the fact that it’s lighter and so, so tasty!
    Thanks, Shawna and Ella. You did it again ❣️

    1. Shawna Clark says:

      Hi Alex, I’m so happy you loved the mac and cheese, and I love hearing that it was a hit with your family! It’s one of our favorites, too. Thanks for taking the time to leave a review!

  2. Shawna Clark says:

    5 stars
    This Butternut Squash Mac and Cheese is a fantastic combo of creamy, cheesy comfort and subtly sweet squash! It’s rich, flavorful, and one of my favorite twists on a classic comfort food.