When fall arrives, there’s nothing more comforting than a hearty dish of Butternut Squash Mac and Cheese. This version combines the creamy sweetness of roasted squash with the richness of cheddar, Gruyere, and pecorino cheeses. Make it easy on yourself by roasting the squash and shallots up to four days ahead.

- Cuisine: American
- Prep Time: 20 minutes
- Cook Time: 60 minutes
- Total Time: 80 minutes
- Servings: 6
Why You’ll Love This Recipe
- Perfectly balances creamy and cheesy elements with a hint of sweetness from the squash.
- Make-ahead components simplify meal prep.
- Ideal for cozy gatherings or weeknight dinners.
- Customizable with your favorite pasta shapes and gluten-free options.
Ingredients
- 1 large butternut squash: Provides natural sweetness and creamy texture. Roast ahead for convenience.
- 2 shallots, roughly chopped (⅔ cup): Adds subtle onion flavor. Substitute with a small yellow onion if unavailable.
- 1 pound shell pasta (or pipe rigate or elbows*): Perfect for holding creamy sauces. Use gluten-free pasta if needed.
- ¼ cup extra-virgin olive oil, plus more for drizzling: Helps roast the squash and binds the topping together.
- 2 teaspoons balsamic vinegar: Adds depth to the sauce. Replace with apple cider vinegar for a lighter flavor.
- 1½ teaspoons sea salt: Enhances all the flavors.
- 1 teaspoon onion powder: Intensifies the savory taste.
- ½ teaspoon garlic powder: Adds mild garlic flavor.
- ½ teaspoon ground sage: Pairs perfectly with squash, offering earthy notes.
- ¼ teaspoon nutmeg: Complements the creamy sauce with warmth and spice.
- Freshly ground black pepper: Adds a touch of heat.
- 1½ cups unsweetened almond milk: Keeps the dish creamy without dairy. Substitute with any milk of choice.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): Provides sharp, tangy flavor.
- 6 ounces grated Gruyere cheese (about 2½ cups): Adds nutty richness to the sauce.
- 1½ ounces finely grated pecorino cheese (½ cup): Gives a salty, bold finish to the dish.
- ¾ cup panko breadcrumbs*: Forms a crispy topping. Use gluten-free panko if needed.
- 1½ teaspoons extra-virgin olive oil: Coats the panko for a crunchy texture.
How to Make It
Step 1: Roast the Squash and Shallots
Preheat your oven to 425°F. Line a baking sheet with parchment paper and grease a 9×13-inch baking dish. Cut the squash in half lengthwise and remove the seeds. Drizzle with olive oil, season with salt and pepper, and place cut-side down on the baking sheet. Wrap shallots in foil with olive oil and a sprinkle of salt. Roast for 30 to 45 minutes until the squash is tender.
Step 2: Prepare the Topping
In a small bowl, combine panko breadcrumbs and olive oil. Mixing helps the breadcrumbs brown evenly under the broiler. Set aside until needed.
Step 3: Cook the Pasta
Bring a large pot of salted water to a boil. Cook your pasta until al dente, following the package instructions. Reserve 1½ cups of starchy pasta water, as it helps bind the sauce later. Drain the pasta and set aside.
Step 4: Blend the Sauce
Measure 2 cups of the roasted squash flesh. Blend it with the reserved pasta water, roasted shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and pepper until smooth and creamy. The consistency should be pourable yet thick enough to coat the pasta.
Step 5: Combine the Ingredients
Return the pot to the stove over medium heat. Add almond milk and heat through. Gradually whisk in the squash sauce and cheeses, ensuring each cheese melts completely before adding more. Stir continuously to achieve a smooth, creamy texture. Mix in the cooked pasta until fully coated.
Step 6: Broil the Top
Preheat the broiler. Transfer the cheesy pasta to the prepared baking dish. Top with pean panko mixture. Broil for 5 to 10 minutes until the topping is golden brown and crispy. Let it rest for 15 minutes to set before serving.
Recipe FAQs
Can I make this recipe ahead of time?
Yes, you can prepare the roasted squash and shallots up to four days in advance. Store them in an airtight container in the refrigerator. The entire dish can be assembled ahead and refrigerated, but wait to add the crumb topping and broil just before serving for maximum crispiness.
What is a good substitute for Gruyere cheese?
If Gruyere cheese is unavailable, you can substitute Swiss cheese or a combination of Emmental and mild provolone. Both options offer similar nutty and creamy characteristics.
Is there a way to make this dish dairy-free?
Absolutely! Replace the cheddar, Gruyere, and pecorino with your favorite dairy-free cheese alternatives. Ensure they melt well to maintain the creamy texture of the sauce.