Name: Cheesy Baked Butternut Squash Mac and Cheese
Prep time: 20 min
Cook time: 1 h 20 min
Total time: 1 h 40 min
Cuisine: American
Ingredients: 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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Cheesy Baked Butternut Squash Mac and Cheese is a cozy, comforting dish that’s not only packed with flavor but also has a delightful creamy texture that wraps around shell pasta beautifully. This version of mac and cheese features sweet, roasted butternut squash blended into a luscious cheese sauce, making it feel indulgent yet guilt-free. The hint of sage and nutmeg adds depth, while the crunchy panko topping brings that irresistible contrast we all love. Trust me, once you’ve tried this, traditional mac and cheese will never look the same.

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
Recipe FAQs
Cheesy Baked Butternut Squash Mac and Cheese

Cheesy Baked Butternut Squash Mac and Cheese

I first stumbled upon this recipe during a chilly fall evening when I craved something warm and cheesy yet nutritious. It quickly became a family favorite — a dish that brings everyone to the table, smiles guaranteed. There’s something truly magical about incorporating seasonal ingredients like butternut squash into a classic comfort food. You get all the creamy, cheesy goodness of mac and cheese, with the added bonus of vitamins, minerals, and color. Plus, it’s naturally colorful and decadent, making it a feast for the eyes as well as the belly. You won’t want to miss out on this Cheesy Baked Butternut Squash Mac and Cheese, so let’s jump in!

Why You’ll Love This Recipe

Simple & Quick: Ready in about 80 minutes, it’s an easy way to impress your friends or family.
Irresistible Flavor: The sweet roasted butternut squash adds an unexpected twist, while sharp cheddar, Gruyere, and Pecorino lend a rich taste.
Eye-Catching Appeal: The vibrant yellow-orange hue complements any table setting, making it a showstopper.
Flexible Serving: Perfect for a weeknight dinner, potluck gatherings, or even holiday feasts.
Diet-Friendly Options: Easily adaptable for gluten-free diets by swapping pasta types!

Ingredients You’ll Need

1 large butternut squash: This key ingredient adds natural sweetness and creaminess. Look for ones that feel heavy and have smooth skin.
2 shallots, roughly chopped (⅔ cup): Shallots offer a milder onion flavor that compliments the squash. You could substitute with yellow onions if necessary.
1 pound shell pasta or pipe rigate or elbows: I recommend shell pasta for its ability to hold the cheese sauce.
¼ cup extra-virgin olive oil: Adds richness and flavor to both the squash and the breadcrumb topping.
2 teaspoons balsamic vinegar: A splash adds brightness to the creamy sauce.
1½ teaspoons sea salt: Enhances the flavors of all ingredients; adjust based on your taste.
1 teaspoon onion powder: Adds even more depth to the flavor.
½ teaspoon garlic powder: Because who doesn’t love garlic in mac and cheese?
½ teaspoon ground sage: This herb perfectly complements the flavor of the squash.
¼ teaspoon nutmeg: A pinch rounds out the flavor profile, especially in creamy dishes.
Freshly ground black pepper: Adds a mild heat that elevates the dish.
1½ cups unsweetened almond milk: Creates a lighter sauce; feel free to use dairy milk if preferred.
6 ounces grated sharp cheddar cheese (about 2½ cups): For that quintessential mac and cheese tang.
6 ounces grated Gruyere cheese (about 2½ cups): It adds complexity and creaminess.
1½ ounces finely grated Pecorino cheese (about ½ cup): A salty kick that balances the flavor.
¾ cup panko breadcrumbs: For a crunchy topping; could use crushed crackers as an alternative.
1½ teaspoons extra-virgin olive oil: For drizzling on the breadcrumbs to help them brown perfectly.

How to Make Cheesy Baked Butternut Squash Mac and Cheese

Preheat the oven: Set your oven to 425°F. This is the perfect temperature to roast the squash and shallots, creating a caramelized sweetness.

Prepare the squash: Split the butternut squash in half lengthwise, scooping out the seeds. Drizzle the cut sides with olive oil and sprinkle with sea salt and freshly ground black pepper. Place the squash cut-side down on a parchment-lined baking sheet. Wrap the shallots in foil, drizzle with olive oil, season with a bit of salt, and place on the baking sheet alongside the squash. Roast for about 30 to 45 minutes, or until the squash is fork-tender and the shallots are fragrant.

Whip up the topping: In a small bowl, combine ¾ cup panko breadcrumbs with 1½ teaspoons extra-virgin olive oil. Toss them well so every breadcrumb is coated, creating a delightful crunch.

Cook the pasta: Bring a large pot of salted water to a boil, then add your 1 pound shell pasta, cooking until al dente according to package instructions. When ready, reserve 1½ cups of the starchy pasta water before draining the pasta.

Blend a creamy sauce: Measure out 2 cups of the cooked, soft squash flesh and put it into a blender. Add the reserved 1½ cups pasta water, the roasted shallots, 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 everything until smooth and creamy, creating a delectable sauce.

Combine the flavors: Return the pasta pot to the stove and heat 1½ cups unsweetened almond milk over medium heat. Stir the blended squash sauce into the almond milk and cook for about 3 minutes. Gradually whisk in the 6 ounces grated sharp cheddar cheese, 6 ounces grated Gruyere cheese, and 1½ ounces finely grated Pecorino cheese. Whisk continuously until each addition is fully melted and the sauce is velvety.

Bake it: Pour the cheese-coated pasta into the prepared 9×13-inch baking dish. Top with your seasoned panko mixture. Then, broil on high for 5 to 10 minutes until the topping is crisp and golden brown, watching closely to avoid burning.

Let it stand: Allow your Cheesy Baked Butternut Squash Mac and Cheese to sit for 15 minutes before serving. This rest time helps the flavors meld beautifully.

Storing & Reheating

Store any leftovers in an airtight container in the refrigerator for up to 4 days. If you’d like to freeze it, portion it into freezer-safe containers or bags, keeping it good for up to 3 months. When you’re ready to enjoy the leftovers, reheat in the oven at 350°F for about 20 minutes, or until warmed through. Keep in mind that the texture might change slightly, but a splash of almond milk can help refresh the creaminess.

Chef’s Helpful Tips

To avoid mushy pasta, make sure to cook it al dente; it will continue cooking in the oven.
Let your cheeses come to room temperature before adding them — this helps them melt smoothly.
If the sauce seems thick when adding cheese, don’t hesitate to incorporate a bit more pasta water for the perfect consistency.
Experiment with herbs! Fresh thyme or rosemary can elevate the dish even more.
For a twist, consider adding pre-cooked bacon or vegetables like spinach for an extra layer of flavor.

Cheesy Baked Butternut Squash Mac and Cheese combines the nostalgia of childhood comfort food with a nutritious spin. The richness of the cheeses, paired with the natural sweetness of the squash, creates a dish that is both indulgent and wholesome. While simple enough for a weeknight meal, it’s elevated enough to impress your guests. I encourage you to get creative — maybe try a different cheese or add a pinch of your favorite spice. Enjoy this delightful dish as you savor each creamy, cheesy bite!

Recipe FAQs

Can I use other types of pasta?

Absolutely! While shell pasta holds the sauce wonderfully, you can use elbow macaroni, spiral pasta, or even gluten-free pasta. Just make sure to adjust the cooking time according to the package.

How can I make this dish vegan?

You can make this dish vegan by using plant-based cheese alternatives, swapping almond milk for another non-dairy milk, and omitting the Pecorino. Just check that all ingredients are vegan-friendly!

What if I don’t have shallots?

If you don’t have shallots, feel free to substitute with yellow onions or even green onions. They will give a slightly different flavor, but it’ll still be delicious.

How do I know when the butternut squash is done roasting?

The butternut squash should be fork-tender and slightly caramelized at the edges, usually taking about 30 to 45 minutes in the oven. If you can easily scoop out the flesh with a spoon, it’s ready to go!