Butternut Squash Mac and Cheese is the ultimate comfort food with a wholesome twist. Creamy, velvety cheese sauce meets the natural sweetness of roasted butternut squash, creating a rich and indulgent dish. The tender pasta absorbs every bit of flavor, while a golden, crispy topping adds the perfect crunch. In just 20 minutes of prep and an hour of baking, you’ll have a meal that’s both comforting and nourishing.
This recipe is a feast for the senses, blending savory and sweet in every bite. The smooth, luscious texture of the sauce pairs beautifully with the al dente pasta, making it irresistible. Whether it’s a cozy weeknight dinner or a crowd-pleasing side, this dish delivers warmth and satisfaction. It’s proof that comfort food can be both delicious and wholesome.
Ingredients for Butternut Squash Mac and Cheese
- 1 large butternut squash (halved and seeded)
- 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, to taste
- 1½ cups unsweetened almond milk (or any milk of choice)
- 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)
- For the topping:
- ¾ cup panko breadcrumbs
- 1½ teaspoons extra-virgin olive oil
Step-by-Step Instructions
- Preheat the oven to 425°F. Line a baking sheet with parchment paper and grease a 9×13-inch baking dish.
- Prepare the squash: Slice the squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and sprinkle with salt and pepper. Place cut side down on the baking sheet.
- Roast the shallots: Place the shallots on a piece of foil, drizzle with olive oil, sprinkle with salt, and wrap tightly. Place on the baking sheet with the squash. Roast for 30 to 45 minutes, or until the squash is soft.
- Make the topping: In a small bowl, combine the panko and olive oil. Toss to coat evenly and set aside.
- Cook the pasta: Bring a large pot of salted water to a boil. Cook the pasta according to the package instructions until al dente. Reserve 1½ cups of the starchy pasta water before draining.
- Blend the sauce: Measure 2 cups of the cooked squash flesh and transfer to a blender. Add the reserved pasta water, roasted shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until smooth and creamy.
- Heat the sauce: Return the pasta pot to the stove and heat the almond milk over medium heat. Stir in the squash sauce and cook, stirring often, for 3 minutes, or until warmed through.
- Add the cheese: Whisking constantly, gradually add the cheddar, Gruyere, and pecorino cheeses, ensuring each addition is fully melted before adding the next. Whisk until the sauce is creamy and smooth.
- Combine pasta and sauce: Add the cooked pasta to the cheese sauce and stir until evenly coated.
- Broil the topping: Preheat the oven broiler. Transfer the pasta mixture to the prepared baking dish and sprinkle with the panko topping. Broil for 5 to 10 minutes, or until the topping is golden brown and crispy.
- Let it rest: Allow the dish to stand for 15 minutes before serving. Enjoy!
Perfect Pairings: Serving Suggestions
This Butternut Squash Mac and Cheese is a star on its own, but pairing it with a crisp green salad or roasted Brussels sprouts adds a fresh contrast. For a heartier meal, serve alongside grilled chicken or sausage. A glass of dry white wine or sparkling cider complements the dish beautifully.
Make It Ahead: Storage and Reheating Tips
Store leftovers in an airtight container in the fridge for up to 3 days. To reheat, place in a baking dish, add a splash of almond milk, and cover with foil. Bake at 350°F for 15-20 minutes, or until warmed through. For a quick fix, microwave individual portions with a damp paper towel to retain moisture.
Switch It Up: Recipe Variations
Try swapping the shell pasta for whole wheat or gluten-free options. For a smoky twist, add crumbled bacon or smoked paprika to the sauce. If you’re dairy-free, use vegan cheese and skip the pecorino. You can also experiment with different herbs like thyme or rosemary for a unique flavor profile.
Time-Saving Hacks
Roast the squash and shallots a day ahead to cut prep time. Use pre-grated cheese to save a few minutes. If you’re in a rush, skip the broiling step and serve the mac and cheese straight from the stovetop—it’s just as delicious!
Essential Equipment Notes
A high-speed blender ensures a silky-smooth squash sauce. A sturdy 9×13-inch baking dish is perfect for broiling the topping to golden perfection. Don’t forget a good whisk for melting the cheese evenly into the sauce!
Butternut Squash Mac and Cheese
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
For the topping
- ¾ cup panko breadcrumbs
- 1½ teaspoons extra-virgin olive oil
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 the cut sides with olive oil and sprinkle with salt and pepper. Place cut side down on the baking sheet. Place the shallots on a piece of foil, drizzle with olive oil and sprinkle with salt, and wrap tightly. Place on the baking sheet and roast for 30 to 45 minutes, or until the squash is soft.
- Make the topping: In a small bowl, place the panko and olive oil. Toss to combine.
- Bring a large pot of salted water to a boil. Prepare the pasta according to the package instructions, cooking until al dente. Reserve 1½ cups of the starchy pasta water before draining.
- Measure 2 cups of the cooked, soft squash flesh and transfer to a blender with the 1½ cups pasta water, the shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.
- Return the pasta pot to the stove and heat the almond milk over medium heat. Stir in the squash sauce and cook, stirring often, for 3 minutes, or until warmed through. Whisking constantly, gradually add the cheddar, Gruyere, and pecorino cheeses, making sure each addition is fully melted before adding the next. Whisk until all the cheese is fully melted and the sauce is creamy, then add the pasta and stir until coated.
- Preheat the oven broiler and transfer the pasta to the prepared baking dish. Top with the panko and broil for 5 to 10 minutes, or until the topping is crisp and browned.
- Let stand for 15 minutes before serving.