Discover a creamy, delicious Butternut Squash Mac and Cheese that’s secretly healthy! This comforting twist on macaroni and cheese is perfect for satisfying cravings while staying nutritious.

A family of four enjoying lunch with a close-up focus on a bowl of creamy butternut squash mac and cheese, featuring its golden crispy top.

Butternut Squash Mac and Cheese

This baked mac and cheese is a crowd-pleaser that the whole family will love—kids and adults alike! Made with a blend of cheeses layered in the dish and melted into a creamy, rich cheese sauce, it’s the ultimate comfort food. Perfect for cozy dinners or as a standout holiday side dish!

What Makes This Butternut Squash Mac and Cheese So Irresistible

This Butternut Squash Mac and Cheese takes the comfort of the classic we all adore and sneaks in a boost of nutrients! Made with wholesome ingredients like whole-wheat noodles, three irresistible cheeses (Gruyere, cheddar, and Parmesan), caramelized shallots, and velvety butternut squash, it’s creamy, cozy, and oh-so-nourishing. My sisters and I are obsessed—it’s our new go-to! Pair it with a fresh green salad for the ultimate anytime meal.

How To Make Butternut Squash Mac and Cheese

Once you have all these ingredients ready, follow the instructions, and you’ll see how easy this is! If you’ve never made homemade mac and cheese before, it might feel a little intimidating, but don’t worry—we’ve got you covered. We’ll guide you step by step to make sure your Butternut Squash Mac and Cheese turns out creamy, cozy, and absolutely delicious. Trust me, once you try this, you’ll never look at boxed mac and cheese the same way again!

Ingredients

Here’s what you’ll need to whip up this creamy, nourishing Butternut Squash Mac and Cheese:

  • 1 pound cubed butternut squash
  • 10 ounces whole wheat elbow pasta
  • 1 ½ cups low-sodium vegetable broth, divided
  • ½ teaspoon onion powder
  • ½ teaspoon garlic powder
  • 1 medium shallot, minced
  • 2 cups skim milk
  • ¼ cup all-purpose flour
  • 1 tablespoon unsalted butter
  • ½ cup shredded Gruyere cheese
  • ½ cup shredded cheddar cheese
  • 2 tablespoons freshly grated Parmesan cheese
  • ¼ cup panko breadcrumbs
  • Olive oil spray
  • salt
  • Chopped chives (optional, for garnish)

Once you have all these ingredients ready, it’s time to dive in! Follow the instructions step by step, and you’ll have the most delicious homemade Butternut Squash Mac and Cheese on your table in no time.

Instructions

Here’s how to make this creamy Butternut Squash Mac and Cheese step by step:

A 9x11-inch glass baking dish sprayed with oil, set on a wooden countertop, with a preheated oven at 375°F visible in the background, along with measuring cups and a towel.

1. Prep your oven and baking dish: Preheat the oven to 375°F. Spray a 9” x 11” glass baking dish with olive oil spray and set aside.

Chunks of squash boiling in a large stainless steel pot with salted water, steam rising, set in a cozy kitchen with a wooden countertop and tiled backsplash.

2. Cook the butternut squash: Bring a large pot of salted water to a boil. Add the squash and cook for 5–6 minutes, or until fork-tender. Use a slotted spoon to transfer the squash to a blender.

3. Cook the pasta: Add the pasta to the same boiling water and cook according to the package directions. Drain when done and return to the pot.

A kitchen scene showing a pot of cooked squash being lifted with a slotted spoon and transferred into a blender on a clean countertop.

4. Blend the squash sauce: To the blender with the squash, add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon kosher salt, and a pinch of black pepper. Blend until smooth and creamy.

5. Make the breadcrumb topping: In a small bowl, mix together the breadcrumbs, Parmesan, ¼ teaspoon salt, and a little black pepper. Set aside.

In a medium saucepan, melt the butter over medium heat. Add the minced shallots and sauté for 2 minutes. Sprinkle the flour evenly over the shallots and cook for 1 minute, stirring constantly.

6. Make the cheese sauce: In a medium saucepan, melt the butter over medium heat. Add the minced shallots and sauté for 2 minutes. Sprinkle the flour evenly over the shallots and cook for 1 minute, stirring constantly.

7. Add liquids: Whisk in the remaining 1 cup vegetable broth and the skim milk. Bring to a boil, then reduce heat to medium-low and cook for 5 minutes, whisking often, until the sauce thickens.

Whisking Gruyere, cheddar, and pureed squash in a saucepan with black pepper and kosher salt in a cozy kitchen setting.

8. Add cheese and squash: Remove the pot from the heat and whisk in the Gruyere, cheddar, pureed squash, 1 ½ teaspoons kosher salt, and more black pepper to taste.

9. Combine pasta and sauce: Pour the sauce over the cooked pasta and gently mix until well coated. Transfer the mixture to the prepared baking dish.

A casserole dish with a breadcrumb topping, golden brown from broiling, inside a glowing oven during the final stage of baking.

10. Bake and broil: Sprinkle the breadcrumb mixture evenly over the top. Bake for 25 minutes, then switch the oven to high broil for 2–3 minutes, or until the topping is golden brown.

Variations

If you’re looking to switch things up with your Butternut Squash Mac and Cheese, here are some fun and delicious variations to try!

  • Bacon: Bacon lovers, this one’s for you! Add some crispy, crumbled bacon on top or mix it right into the mac and cheese for that perfect salty crunch.
  • Stovetop: Not in the mood to bake? No problem! Simply cook your pasta until al dente (follow the package instructions), and use about 3–3 ½ cups of cheese. Skip the baking step—just mix all the cheese into your sauce and combine with the pasta for a stovetop version.
  • Different Toppings: If you love a crispy, cheesy top, you can stick with the classic cheese layer, but we also love mixing 1 cup of panko breadcrumbs with 2 tablespoons of melted butter as a crunchy topping. Or try crushed Ritz crackers (1 cup) mixed with 2 tablespoons of butter—it’s a total game-changer!
  • Different Baking Times: While the recipe calls for a lower baking temperature and time, feel free to adjust it to your family’s preference. I often bake mine at 350°F for 30 minutes, then broil for 2–3 minutes to get that perfect golden, cheesy “crust.”

Butternut Squash Mac and Cheese—a healthier twist on your classic mac and cheese that’s so creamy and delicious, no one will ever guess it’s good for you! With the perfect balance of cheesy goodness and the natural sweetness of butternut squash, this dish is comfort food at its best, but with a nutritious twist!

More Butternut Squash Recipes

Close-up of a bowl of creamy butternut squash mac and cheese with a golden crispy top and sprinkled breadcrumbs, ready to serve.

Butternut Squash Mac and Cheese Recipe

Pamela J. Willis
Butternut Squash Mac and Cheese—a healthier twist on your classic mac and cheese that’s so creamy and delicious, no one will ever guess it’s good for you! With the perfect balance of cheesy goodness and the natural sweetness of butternut squash, this dish is comfort food at its best, but with a nutritious twist!
Prep Time 20 minutes
Cook Time 1 hour
Total Time 1 hour 20 minutes
Course Brunch, Lunch, Side Dish
Cuisine American
Servings 8 people
Calories 267 kcal

Ingredients
  

  • 1 pound cubed butternut squash
  • 10 ounces whole wheat elbow pasta
  • 1 ½ cups low-sodium vegetable broth divided
  • ½ teaspoon onion powder
  • ½ teaspoon garlic powder
  • 1 medium shallot minced
  • 2 cups skim milk
  • ¼ cup all-purpose flour
  • 1 tablespoon unsalted butter
  • ½ cup shredded Gruyere cheese
  • ½ cup shredded cheddar cheese
  • 2 tablespoons freshly grated Parmesan cheese
  • ¼ cup panko breadcrumbs
  • Olive oil spray
  • Kosher salt
  • Chopped chives optional, for garnish

Instructions
 

  • Preheat the oven to 375°F. Spray a 9” x 11” glass baking dish with olive oil spray and set aside.
  • Bring a large pot of salted water to a boil. Add the squash and cook for 5–6 minutes, or until fork-tender. Use a slotted spoon to transfer the squash to a blender.
  • Add the pasta to the same boiling water and cook according to the package directions. Drain when done and return to the pot.
  • To the blender with the squash, add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon kosher salt, and a pinch of black pepper. Blend until smooth and creamy.
  • In a small bowl, mix together the breadcrumbs, Parmesan, ¼ teaspoon salt, and a little black pepper. Set aside.
  • In a medium saucepan, melt the butter over medium heat. Add the minced shallots and sauté for 2 minutes. Sprinkle the flour evenly over the shallots and cook for 1 minute, stirring constantly.
  • Whisk in the remaining 1 cup vegetable broth and the skim milk. Bring to a boil, then reduce heat to medium-low and cook for 5 minutes, whisking often, until the sauce thickens.
  • Remove the pot from the heat and whisk in the Gruyere, cheddar, pureed squash, 1 ½ teaspoons kosher salt, and more black pepper to taste.
  • Pour the sauce over the cooked pasta and gently mix until well coated. Transfer the mixture to the prepared baking dish.
  • Sprinkle the breadcrumb mixture evenly over the top. Bake for 25 minutes, then switch the oven to high broil for 2–3 minutes, or until the topping is golden brown.

Notes

Nutrition Serving: 1 cup

Calories: 267 kcal, Carbohydrates: 43 g, Protein: 13 g, Fat: 7 g, Saturated Fat: 4 g, Cholesterol: 21 mg, Sodium: 462 mg, Fiber: 4.5 g, Sugar: 5 g
Keyword Creamy mac and cheese, Fall-inspired recipe, Healthy Comfort Food, Nutritious mac and cheese, Vegetarian pasta dish

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