If you’re craving a comforting dish that brings a fresh twist to an old favorite, this Butternut Squash Mac and Cheese Recipe is exactly what you need. Creamy, cheesy, and full of naturally sweet butternut squash, it’s a perfect balance of indulgence and wholesome goodness. The vibrant orange hue from the squash not only brightens your plate but also adds a velvety texture that’s simply irresistible. This recipe transforms traditional mac and cheese into something delightful and nourishing, making it ideal for cozy dinners or gatherings with friends.

Ingredients You’ll Need
This Butternut Squash Mac and Cheese Recipe uses a handful of simple ingredients, each playing a key role in building flavor, creaminess, and that inviting golden crust. Everything you need is easy to find, and the combination creates a dish that’s both healthy and satisfying.
- Butternut squash, 1 pound cubed: Adds natural sweetness and a creamy texture that blends beautifully with the cheese sauce.
- Chopped chives (optional): Adds a fresh, mild oniony flavor as a garnish that brightens every bite.
- Olive oil spray: Used for prepping the baking dish to ensure the mac and cheese doesn’t stick while baking.
- Kosher salt: Essential for seasoning every layer, enhancing all the ingredients’ inherent flavors.
- Whole wheat elbow pasta, 10 ounces: Offers a slightly nutty flavor and sturdy texture that holds up perfectly under the rich sauce.
- Low sodium vegetable broth, 1 ½ cups (divided): Brings depth and moisture to the sauce without overwhelming the delicate flavors.
- Onion powder, ½ teaspoon: Provides a subtle depth without bouncing the dish with fresh onion sharpness.
- Garlic powder, ½ teaspoon: Infuses warmth and an earthy note that complements the squash and cheese.
- Panko breadcrumbs, ¼ cup: Creates a crunchy topping that contrasts wonderfully with the creamy interior.
- Unsalted butter, 1 tablespoon: The base for our roux, which thickens the cheese sauce to perfection.
- Medium shallot, minced: Adds a sweet and delicate onion flavor, gently mellowed by sautéing.
- All-purpose flour, ¼ cup: Thickens the sauce, giving it that satisfying, silky texture.
- Skim milk, 2 cups: The creamy liquid that makes the sauce luscious without feeling too heavy.
- Freshly grated Parmesan cheese, 2 tablespoons: Adds a sharp, nutty flavor that enhances the cheese blend and the breadcrumb topping.
- Shredded Gruyere cheese, ½ cup: Offers a rich, slightly sweet and nutty dimension to the sauce.
- Shredded cheddar cheese, ½ cup: Traditional mac and cheese flavor, melty and sharp, balancing the creaminess perfectly.
How to Make Butternut Squash Mac and Cheese Recipe
Step 1: Preheat and Prep
Start by preheating your oven to 375 degrees Fahrenheit. Make sure to spray a 9” x 11” glass baking dish with olive oil spray to prevent sticking and help the topping get nice and crispy during baking.
Step 2: Cook the Butternut Squash
Bring a large pot of salted water to a boil and add the cubed butternut squash. Boil for about 5-6 minutes until the squash is tender but not mushy—this ensures it will puree smoothly. Once done, drain and transfer the squash to a blender for the next step.
Step 3: Cook the Pasta
Using the same pot of boiling water, cook your whole wheat elbow pasta following the package directions until al dente. Drain the pasta and return it to the pot so it’s ready to be combined with the sauce.
Step 4: Puree the Squash
Add ½ cup of the vegetable broth, onion powder, garlic powder, 1 teaspoon of kosher salt, and a pinch of black pepper to the blender with the cooked butternut squash. Blend everything until super smooth and creamy. This puree will provide the heart of your velvety cheese sauce.
Step 5: Make the Breadcrumb Topping
In a small bowl, mix the panko breadcrumbs, Parmesan cheese, ¼ teaspoon of salt, and a pinch of pepper. This mixture will be sprinkled on top to give your dish a golden, crunchy finish after baking.
Step 6: Make the Cheese Sauce
In a medium saucepan, melt the butter over medium heat. Sauté the minced shallot for about 2 minutes until fragrant and translucent. Next, sprinkle in the flour and cook for another minute while stirring constantly. Gradually whisk in the remaining 1 cup of vegetable broth and 2 cups of milk. Bring this mixture to a boil, then reduce the heat to low and simmer for 5 minutes, stirring frequently until the sauce thickens.
Step 7: Combine Sauce and Squash Puree
Remove the saucepan from heat and stir in the Gruyere and cheddar cheeses until melted and smooth. Then, whisk in the pureed butternut squash along with 1 ½ teaspoons salt and a good crack of black pepper. The sauce should be creamy, flavorful, and luscious.
Step 8: Assemble and Bake
Add the cheese sauce to the cooked pasta and gently mix until every noodle is coated with that glorious squash-cheese blend. Transfer the mixture to your prepared baking dish, spreading it evenly. Sprinkle the breadcrumb mixture on top, and bake for 25 minutes. For a perfectly golden crust, switch the oven to broil and cook for 2-3 minutes more, watching carefully so it doesn’t burn.
How to Serve Butternut Squash Mac and Cheese Recipe

Garnishes
A sprinkle of chopped chives on top adds a fresh, green pop of color and a mild onion flavor that brightens the entire dish. It’s a simple touch that makes the mac and cheese feel extra special and vibrant on the plate.
Side Dishes
This Butternut Squash Mac and Cheese Recipe pairs beautifully with crisp green salads, roasted Brussels sprouts, or even a tangy coleslaw. These sides add texture contrasts and fresh notes that balance the richness of the creamy mac and cheese, making your meal rounded and satisfying.
Creative Ways to Present
Try serving this mac and cheese in individual ramekins for an adorable, personalized touch perfect for entertaining. Or scoop it into hollowed-out mini pumpkins for a festive autumn presentation that will wow your guests visually and deliciously.
Make Ahead and Storage
Storing Leftovers
Store any leftover Butternut Squash Mac and Cheese Recipe in an airtight container in the refrigerator. It will stay good for up to 3-4 days, allowing you to enjoy the comforting flavors again without cooking from scratch.
Freezing
If you want to save this dish for longer, it freezes well. Transfer cooled mac and cheese to a freezer-safe container or bag, and freeze for up to 2 months. Thaw overnight in the fridge before reheating to keep the texture intact.
Reheating
Reheat leftovers gently in the oven at 350 degrees Fahrenheit, covered to prevent drying out, for about 15-20 minutes. You can also microwave single servings, adding a splash of milk to refresh the creamy consistency as you warm it.
FAQs
Can I use regular pasta instead of whole wheat?
Absolutely! Regular pasta works perfectly for this Butternut Squash Mac and Cheese Recipe. Whole wheat adds a nuttier flavor and extra fiber, but feel free to use whatever pasta you prefer or have on hand.
Is it possible to make this recipe dairy-free?
Yes, you can adapt it by substituting the milk with unsweetened plant-based milk and using dairy-free cheese alternatives. The butternut squash puree helps keep the sauce creamy even without traditional dairy.
How do I know when the butternut squash is cooked enough for pureeing?
The squash should be tender enough that you can easily pierce a cube with a fork. Boiling for 5-6 minutes usually achieves the right softness without turning the squash mushy.
Can I prepare the cheese sauce a day ahead?
Definitely! Making the sauce ahead saves time. Just allow it to cool, cover tightly, and refrigerate. When ready to bake, combine it with the pasta and assemble as directed.
What can I add for extra protein?
Adding cooked chicken, crispy bacon bits, or even some cooked lentils mixed in with the pasta can boost the protein content while complementing the rich flavors of this Butternut Squash Mac and Cheese Recipe.
Final Thoughts
This Butternut Squash Mac and Cheese Recipe is truly a game-changer in the world of comfort food. With its creamy squash-infused sauce, melty cheeses, and crunchy topping, every bite feels like a warm hug. It’s simple enough to make for weeknight dinners but impressive enough to serve to guests. Give it a try—you might just find your new favorite twist on a classic!
Print
Butternut Squash Mac and Cheese Recipe
- Prep Time: 15 minutes
- Cook Time: 1 hour
- Total Time: 1 hour 15 minutes
- Yield: 8 servings
- Category: Main Course
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
This creamy and comforting Butternut Squash Mac and Cheese combines tender whole wheat pasta with a velvety pureed butternut squash cheese sauce, topped with a crispy Parmesan breadcrumb crust. It’s a healthier twist on classic mac and cheese, featuring wholesome ingredients and a rich blend of Gruyere, cheddar, and Parmesan cheeses. Perfect for a cozy family meal or to impress guests with a nutritious yet indulgent dish.
Ingredients
Main 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
- Kosher salt
- Black pepper
- Olive oil spray
- Chopped chives (optional, for garnish)
Breadcrumb Topping
- ¼ cup panko breadcrumbs
- 1 tablespoon unsalted butter
- 2 tablespoons freshly grated Parmesan cheese
- ¼ teaspoon salt
- Black pepper
Cheese Sauce
- 1 medium shallot, minced
- ¼ cup all-purpose flour
- 2 cups skim milk
- ½ cup shredded Gruyere cheese
- ½ cup shredded cheddar cheese
Instructions
- Preheat and Prep: Preheat the oven to 375°F (190°C). Spray a 9” x 11” glass baking dish lightly with olive oil spray to prevent sticking.
- Cook Squash: Bring a large pot of salted water to a boil. Add the cubed butternut squash and boil until tender, about 5-6 minutes. Once cooked, transfer the squash to a blender for pureeing.
- Cook Pasta: In the same boiling water, add the whole wheat elbow pasta and cook according to package directions until al dente. Drain and return to the pot.
- Puree Squash: To the blender with the cooked squash, add ½ cup of the vegetable broth, onion powder, garlic powder, 1 teaspoon salt, and a pinch of black pepper. Blend until the mixture is perfectly smooth and creamy.
- Make Breadcrumb Topping: In a small bowl, combine the panko breadcrumbs, freshly grated Parmesan cheese, ¼ teaspoon salt, and a pinch of black pepper. Set aside.
- Make Cheese Sauce: Melt the unsalted butter in a medium saucepan over medium heat. Add the minced shallots and sauté for 2 minutes until soft and fragrant. Sprinkle in the flour and cook for 1 more minute to form a roux. Gradually whisk in the remaining 1 cup of vegetable broth and all of the skim milk. Bring the mixture to a gentle boil, then reduce heat and let it simmer for 5 minutes, whisking frequently to prevent lumps and to thicken the sauce.
- Combine Sauce and Squash: Remove the saucepan from heat. Stir in the shredded Gruyere and cheddar cheeses until melted. Then whisk in the pureed squash mixture along with 1 ½ teaspoons salt and freshly cracked black pepper to taste, creating a rich, cheesy squash sauce.
- Assemble and Bake: Add the cheese and squash sauce to the cooked pasta in the pot and gently mix to combine, ensuring the noodles are well coated. Transfer the mixture to the prepared baking dish. Sprinkle the breadcrumb topping evenly over the surface. Bake in the preheated oven for 25 minutes until bubbly and heated through. For a golden, crispy finish, broil the top for 2-3 minutes until the breadcrumbs are lightly browned. Optionally, garnish with chopped chives before serving.
Notes
- Make sure to not overcook the pasta; it will continue cooking slightly in the oven.
- For extra creaminess, you can substitute skim milk with 2% milk or a dairy-free alternative.
- Panko breadcrumbs add a nice crunch, but regular breadcrumbs can be used as a substitute.
- Adjust seasoning with salt and pepper to your taste before baking.
- Leftovers can be stored in an airtight container in the refrigerator for up to 3 days and reheated in the oven or microwave.

