There’s something undeniably comforting about a warm bowl of macaroni and cheese, especially when it incorporates the rich, velvety goodness of roasted butternut squash. This Cheesy Baked Butternut Squash Mac and Cheese elevates a classic dish into a delightful experience for your taste buds. It’s creamy, cheesy, and just the right amount of savory. The sweetness of the butternut squash harmonizes beautifully with the sharp cheddar and nutty Gruyère, creating a macaroni and cheese that feels indulgent while still being a bit healthier than the traditional version. Whether you’re serving it for a cozy family dinner, a potluck with friends, or just when you’re craving some comfort, this recipe is sure to please.

Table of Contents

Why You’ll Love This Recipe
Ingredients You’ll Need
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Storing & Reheating
Chef’s Helpful Tips
Cheesy Baked Butternut Squash Mac and Cheese

Cheesy Baked Butternut Squash Mac and Cheese

I first stumbled upon this recipe during the autumn months when butternut squash was in season, and I was looking for ways to incorporate more vegetables into our meals without sacrificing flavor. This dish exceeded all expectations. With minimal effort, it transforms simple ingredients into a cheesy masterpiece that even the pickiest eaters will devour. The combination of fresh ingredients and a touch of gourmet makes it feel like a restaurant dish, right in your home kitchen. I can’t wait for you to try it!

Why You’ll Love This Recipe

Simple & Quick: Whip this up in just 20 minutes of prep and 80 minutes total cooking time.
Irresistible Flavor: Enjoy a creamy, cheesy sauce infused with nutmeg and sage that brings warmth to every bite.
Eye-Catching Appeal: The beautiful golden crust from panko crumbs makes it visually appealing.
Flexible Serving: Perfect for a family meal, gatherings, or as a comforting side dish.
Diet-Friendly Options: Easily adaptable for gluten-free and dairy-free diets without sacrificing taste.

Ingredients You’ll Need

1 large butternut squash: This is the star of the dish, adding natural sweetness and creaminess to the sauce. Choose one that feels heavy for its size.
2 shallots, roughly chopped (⅔ cup): These bring a mild onion flavor that serves as a great base for the sauce. If you can’t find shallots, you can substitute them with a small onion.
1 pound shell pasta, or pipe rigate or elbows: The shape of the pasta holds the cheesy sauce beautifully. Choose a variety you love or have on hand!
¼ cup extra-virgin olive oil, plus more for drizzling: Adds richness and enhances the flavor of roasted ingredients. Use high-quality olive oil for the best taste.
2 teaspoons balsamic vinegar: This adds a slight tang that helps balance the dish. A red wine vinegar can be used if necessary.
1½ teaspoons sea salt: Essential for enhancing all flavors throughout the recipe.
1 teaspoon onion powder: This amplifies the onion flavor without being too overpowering.
½ teaspoon garlic powder: Provides a hint of garlic aroma, perfect for the sauce.
½ teaspoon ground sage: Works beautifully with butternut squash, giving a warm, earthy flavor.
¼ teaspoon nutmeg: Adds depth to the sauce and complements the squash nicely.
Freshly ground black pepper to taste: For an extra kick, use freshly ground for the best flavor.
1½ cups unsweetened almond milk: Keeps the mixture creamy and adds a subtle nutty flavor; can be swapped for any plant-based or regular milk.
6 ounces grated sharp cheddar cheese (about 2½ cups): This helps achieve that gooey cheesiness everyone loves. Feel free to use mild if preferred.
6 ounces grated Gruyère cheese (about 2½ cups): Adds richness and a nutty flavor profile that works wonderfully.
1½ ounces finely grated pecorino cheese (½ cup): A beautiful finish, it adds a nice salty tang which balances the flavors.
¾ cup panko breadcrumbs: For a delightful crunchy topping. You can use regular breadcrumbs if panko is unavailable.
1½ teaspoons extra-virgin olive oil: To help the breadcrumbs brown beautifully in the oven.

How to Make Cheesy Baked Butternut Squash Mac and Cheese

Preheat oven: Set your oven to 425°F (220°C) to get it nice and hot before baking. Line a baking sheet with parchment paper and grease a 9×13-inch baking dish to make cleanup easier.

Prepare butternut squash: Carefully slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with a little extra-virgin olive oil and sprinkle with salt and freshly ground black pepper. Place the squash cut-side down on the prepared baking sheet, allowing it to roast beautifully.

Roast shallots: Wrap the chopped shallots in a piece of foil, drizzle with olive oil, and sprinkle with salt. Seal the foil tightly, place it on the baking sheet alongside the squash, and roast for 30 to 45 minutes, or until the squash is soft and tender. You’ll know it’s done when a fork easily pierces the flesh.

Make topping: While everything is roasting, prepare the crunchy topping by tossing ¾ cup of panko breadcrumbs with 1½ teaspoons of extra-virgin olive oil in a small bowl. This will give it a lovely golden color when broiled.

Cook pasta: In a large pot, bring salted water to a rolling boil. Add your pound of shell pasta and cook according to package instructions until al dente. Don’t forget to reserve about 1½ cups of that starchy pasta water before draining—it’s gold for making the sauce creamier later on!

Blend squash: When your squash is ready, scoop out 2 cups of the cooked flesh and place it into a blender. Add in the reserved pasta water, roasted shallots, ¼ cup olive oil, 2 teaspoons balsamic vinegar, 1½ teaspoons sea salt, 1 teaspoon onion powder, ½ teaspoon garlic powder, ½ teaspoon ground sage, ¼ teaspoon nutmeg, and several grinds of black pepper. Blend until the mixture is creamy and smooth.

Heat sauce: Return the empty pasta pot to the stove over medium heat and pour in 1½ cups of unsweetened almond milk. Stir in the blended squash mixture and cook for about 3 minutes, stirring often until it’s heated through. Gradually whisk in the 6 ounces of grated sharp cheddar, 6 ounces of grated Gruyère, and 1½ ounces of finely grated pecorino cheese, ensuring each addition fully melts before adding the next. The result should be a delectable melty sauce that beautifully coats the pasta.

Combine & bake: Once your cheese sauce is ready, add your cooked pasta to the pot and gently stir until every piece is coated in the delicious sauce. Now, transfer this creamy goodness into the greased 9×13-inch baking dish. Top it generously with the prepared panko mixture.

Broil: Preheat your oven broiler and place the baking dish under it. Broil for 5 to 10 minutes, watching closely until the topping is crisp and browned. You want to achieve that beautiful golden crust that means this dish is ready for serving.

Cool & serve: Let your Cheesy Baked Butternut Squash Mac and Cheese stand for 15 minutes before digging in. This helps the cheese set a bit and makes for easier serving.

Storing & Reheating

Once cooled, store any leftovers in an airtight container at room temperature for up to 2 hours, or in the refrigerator for up to 4 days. For longer storage, freeze in an airtight container for a maximum of 3 months. To reheat, thaw in the refrigerator overnight, then bake at 350°F (175°C) for about 25 minutes until heated through. Be aware that the texture might change slightly after freezing, but you can refresh it with a splash of almond milk while reheating.

Chef’s Helpful Tips

Avoid overcooking the pasta; al dente is key as it will continue to cook in the oven.
If your sauce feels too thick, add a little extra reserved pasta water or almond milk to reach your desired consistency.
Make it ahead of time! You can prepare it up to the baking step and store it in the fridge overnight, just add 5 extra minutes to the baking time.
Experiment with different cheeses! Fontina or mozzarella can be great additions instead of Gruyère for a different flavor.
For a bit of spice, add a dash of cayenne pepper to your cheese sauce for a little kick.

The combination of comforting flavors and cheesiness makes this dish an absolute winner. You’re bound to be coming back to it time and again, especially when the craving strikes for something warm and satisfying.

Can I use a different type of pasta?

Absolutely! Feel free to substitute shell pasta, pipe rigate, or even elbow macaroni with your favorite pasta shape. Just make sure to adjust the cooking time according to their package instructions.

Can I make it in advance?

Yes! You can prepare the Cheesy Baked Butternut Squash Mac and Cheese ahead of time. Just follow the recipe up until the baking step, then cover and refrigerate overnight. When you’re ready to bake it, add a few extra minutes to the cooking time.

What can I substitute for dairy?

To create a dairy-free version, you can use unsweetened almond milk and replace the cheeses with dairy-free cheese alternatives. Many brands now offer excellent cheesy options that melt well.

How long will leftovers last?

Leftovers can be stored in an airtight container in the fridge for about 4 days. If you’d like to save some for later, it can also be frozen for up to 3 months. Just make sure to reheat thoroughly before serving!

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Cheesy Baked Butternut Squash Mac and Cheese

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Author: Peter
Prep Time: 20 minutes
Cook Time: 80 minutes
Total Time: 1 hour 40 minutes
Yield: 8 servings 1x
Category: Main Dishes
Method: Baking
Cuisine: American

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Description

This Cheesy Baked Butternut Squash Mac and Cheese is a delicious blend of cheeses and roasted butternut squash, making for an easy and comforting dish that everyone will love. Perfect for a quick dinner or a cozy meal!

Ingredients

Scale

1 large butternut squash
2 shallots, roughly chopped (⅔ cup)
1 pound shell pasta, or pipe rigate or elbows*
¼ cup extra-virgin olive oil, plus more for drizzling
2 teaspoons balsamic vinegar
1½ teaspoons sea salt
1 teaspoon onion powder
½ teaspoon garlic powder
½ teaspoon ground sage
¼ teaspoon nutmeg
freshly ground black pepper
1½ cups unsweetened almond milk
6 ounces grated sharp cheddar cheese, about 2½ cups
6 ounces grated gruyere cheese, about 2½ cups
1½ ounces finely grated pecorino cheese, ½ cup
¾ cup panko breadcrumbs*
1½ teaspoons extra-virgin olive oil

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Instructions

Preheat the oven to 425°F, line a baking sheet with parchment paper, and grease a 9×13-inch baking dish.
Slice the squash in half lengthwise and scoop out the seeds. Drizzle olive oil on the cut sides and sprinkle with salt and pepper. Place cut side down on the baking sheet. Wrap the shallots in foil with olive oil and salt and place them on the baking sheet to roast for 30 to 45 minutes, or until the squash is soft.
In a small bowl, combine the panko with olive oil to make the topping.
Bring a large pot of salted water to a boil and cook the pasta until al dente. Reserve 1½ cups of pasta water before draining.
In a blender, combine 2 cups of the soft squash flesh, reserved pasta water, roasted shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.
Heat almond milk in the pasta pot over medium heat. Stir in the squash sauce and heat for about 3 minutes. Gradually whisk in the cheddar, Gruyere, and pecorino cheeses until melted and creamy. Stir in the cooked pasta until well coated.
Transfer the mixture to the prepared baking dish, top with panko, and broil for 5 to 10 minutes, or until the topping is crisp and browned.
Allow to cool for 15 minutes before serving.

Notes

For a gluten-free option, substitute the pasta with a gluten-free pasta alternative.
Feel free to mix in other vegetables like spinach or kale for added nutrition.