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: Comfort Food
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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With its creamy texture and cheesy goodness, Cheesy Baked Butternut Squash Mac and Cheese is much more than your average comfort food. The sweet, nutty flavor of roasted butternut squash perfectly complements the rich cheeses and the familiar pasta shape we love. The vibrant color adds a playful twist to this traditional dish, making it not just delicious but also a feast for the eyes. Whether you’re feeding a hungry family on a chilly evening or impressing guests at a dinner party, this elevated mac and cheese hits all the right notes.

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 cozy autumn gathering. The sight of creamy pasta sprinkled with crispy breadcrumbs had me drooling. One bite ensued into another, and I knew I had to replicate this dreamy dish in my own kitchen. Every layer of flavor—from the sharp tang of cheddar to the subtle sage—created a comforting embrace that lingered long after the last forkful. It’s affordable, easy to whip up, and most importantly, a surefire crowd-pleaser!

Why You’ll Love This Recipe

Simple & Quick: Ready in about 100 minutes, this dish involves straightforward steps, making it perfect for busy weeknights.
Irresistible Flavor: The combination of sweet butternut squash with tangy cheeses creates a creamy, savory experience.
Eye-Catching Appeal: The brilliant orange hue and crunchy topping make it visually stunning.
Flexible Serving: Ideal for weeknight dinners, potlucks, or as a side dish for your seasonal gatherings.
Diet-Friendly Options: Swap the cheeses for vegan alternatives if you want a plant-based adaptation.

Ingredients You’ll Need

1 large butternut squash: This ingredient adds creaminess and a natural sweetness that balances the savory flavors. Look for a firm squash with a smooth skin.
2 shallots, roughly chopped (⅔ cup): Shallots deliver a subtle, sweet onion flavor without overpowering the dish. Substitute with yellow onions if needed.
1 pound shell pasta (or pipe rigate or elbows): The pasta shape helps hold onto the cheesy sauce; choose your favorite type for variety.
¼ cup extra-virgin olive oil: This healthy oil enhances the flavor of roasted vegetables and provides a silky finish in the cheese sauce.
2 teaspoons balsamic vinegar: It adds a tangy depth that balances the sweetness of the squash. Red wine vinegar works in a pinch.
1½ teaspoons sea salt: Essential for enhancing all the flavors in the dish; adjust based on preference.
1 teaspoon onion powder: This amplifies the onion flavor without the extra texture. Feel free to omit if you prefer.
½ teaspoon garlic powder: Adds a warm, fragrant flavor that rounds out the taste.
½ teaspoon ground sage: This herby note gives a warm, comforting feel to the dish. You can substitute with thyme for a different flavor.
¼ teaspoon nutmeg: A pinch of nutmeg enhances the creaminess and depth of the cheese sauce.
Freshly ground black pepper: Adds a perfect pop of heat. Adjust the amount to your preference.
1½ cups unsweetened almond milk: This dairy-free option keeps the dish creamy while being a lighter alternative to whole milk.
6 ounces grated sharp cheddar cheese (about 2½ cups): Gives a rich, tangy flavor. A blend of mild and sharp adds complexity.
6 ounces grated Gruyere cheese (about 2½ cups): Melts beautifully and brings a nutty dimension to the flavor profile.
1½ ounces finely grated pecorino cheese (about ½ cup): This salty cheese elevates the dish with its unique flavor.
¾ cup panko breadcrumbs: Provides a delightful crunch on top. Swap for regular breadcrumbs if panko is unavailable.
1½ teaspoons extra-virgin olive oil: For tossing with the panko to achieve that perfect golden crunch.

How to Make Cheesy Baked Butternut Squash Mac and Cheese

Preheat the oven: Start by setting your oven to 425°F. Line a baking sheet with parchment paper to prevent sticking and grease a 9×13-inch baking dish for easy serving.

Prepare the squash: Carefully slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and sprinkle with salt and pepper. Place the squash halves cut side down on the prepared baking sheet. Next, on a piece of aluminum foil, place the shallots, drizzle them with a bit of olive oil, sprinkle with salt, and wrap tightly. Put the wrapped shallots next to the squash and roast everything for about 30 to 45 minutes, or until the squash flesh feels soft when pierced with a fork.

Make the topping: While your squash and shallots roast, prepare the breadcrumb topping. In a small bowl, mix the panko breadcrumbs with 1½ teaspoons of extra-virgin olive oil until evenly coated. This helps crisp up the breadcrumbs when baked.

Cook the pasta: Bring a large pot of salted water to a boil. Add in your shell pasta and cook according to package instructions until al dente. Before draining, set aside 1½ cups of the starchy cooking water—this will help the sauce cling to the pasta. Drain the pasta and set it aside.

Blend the squash sauce: Measure 2 cups of the roasted squash flesh, and transfer it to your blender. Add the reserved pasta water, roasted shallots, complementing olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and a few grinds of black pepper. Blend until you achieve a creamy consistency—this will be your delightful sauce!

Combine the ingredients: Return the large pot to the stove and pour in 1½ cups of unsweetened almond milk over medium heat. Stir in the blended squash sauce, cooking for about 3 minutes until warmed through. Gradually whisk in the cheddar, Gruyere, and pecorino cheeses, ensuring that each addition melts completely before adding more. Once creamy, add the drained pasta to this cheesy mixture and stir until every piece is coated in the sauce.

Bake the dish: Preheat your oven’s broiler. Pour the macaroni and cheese mixture into the greased 9×13-inch baking dish. Evenly sprinkle the prepared panko topping on top, then place it under the broiler for about 5 to 10 minutes. Watch closely until the topping turns golden brown and crispy.

Let it cool: After baking, allow your Cheesy Baked Butternut Squash Mac and Cheese to sit for 15 minutes before serving. This resting period helps everything set up a bit, making it easier to serve.

Storing & Reheating

To enjoy leftovers, store your mac and cheese at room temperature for up to 2 hours. For longer storage, place it in an airtight container in the refrigerator, where it will keep for about 3-5 days. If you want to freeze it, portion out the mac and cheese in freezer-safe containers or bags, and it will last up to 3 months. For reheating, simply pop it in the oven at 350°F for about 15-20 minutes or until warmed through. Keep in mind that the texture may change slightly, so a quick drizzle of olive oil before reheating can help restore some creaminess.

Chef’s Helpful Tips

To avoid a gummy texture, don’t overcook the pasta; aim for al dente.
Use room temperature cheeses; they’ll melt more smoothly into your sauce.
If your sauce feels too thick, gradually stir in a bit more almond milk or reserved pasta water.
Feel free to throw in some roasted veggies or cooked proteins for an extra boost in flavor and nutrition!
Experiment with different types of cheese based on what you enjoy.
You can prepare the squash puree in advance and store it in the fridge until you’re ready to finish the dish.

There’s no doubt that the comforting flavors of Cheesy Baked Butternut Squash Mac and Cheese are sure to become a beloved staple in your home. The creamy sauce pairs so beautifully with the pasta, while the crispy breadcrumbs provide that satisfying crunch. I encourage you to play with the ingredients and make it your own—perhaps add some herbs or legumes for an extra twist! You’ll soon find this recipe becomes a go-to whenever you crave a cozy meal. Enjoy every delightful bite!

Recipe FAQs

Can I make this mac and cheese ahead of time?

Yes! You can prepare the entire dish up to the baking step. Store it in the fridge, uncovered to allow it to set, and bake it on the day you plan to serve it. Just remember to add a few extra minutes to the baking time since it will be chilled.

Is there a way to make this recipe gluten-free?

Certainly! You can use gluten-free pasta in place of traditional shells, elbows, or rigate. Just make sure to follow the package instructions for best cooking times.

Can I substitute different cheeses?

Absolutely! If you prefer milder flavors, you could replace sharp cheddar with mild cheddar or even a Mexican cheese blend. Just ensure you have a good melting cheese for the silky sauce.

What can I serve with Cheesy Baked Butternut Squash Mac and Cheese?

This dish pairs wonderfully with a fresh side salad, steamed vegetables, or some garlic bread for a comforting meal. You can also enjoy it on its own as a hearty main dish!