
This butternut squash mac and cheese transforms the classic comfort dish into a fall celebration. The sweet, earthy flavor of roasted butternut squash creates a velvety sauce that pairs perfectly with sharp cheddar and nutty Parmesan, while hints of nutmeg and smoked paprika add warmth to every bite.
I created this recipe during a particularly chilly October when my family was craving something cozy but I wanted to incorporate seasonal produce. The beautiful orange hue and subtle sweetness from the squash made it an instant hit that now signals the official start of fall in our home.
Ingredients
- Butternut squash: provides natural creaminess and subtle sweetness that complements the cheese perfectly
- Sharp cheddar cheese: offers that classic mac and cheese flavor while standing up to the squash
- Parmesan cheese: adds a nutty depth that rounds out the sauce
- Nutmeg: enhances the natural sweetness of the squash and adds warmth
- Smoked paprika: brings a subtle smokiness that elevates the entire dish
- Panko breadcrumbs: create an irresistible textural contrast when broiled to golden perfection
Instructions
- Roast the vegetables:
- Begin by preheating your oven to 400°F. Toss the butternut squash cubes and diced onion with olive oil until every piece is lightly coated. Season generously with salt and pepper. Arrange in a single layer on a baking sheet, giving them space to caramelize rather than steam. Roast for 25 to 30 minutes, stirring halfway through, until the edges are golden brown and the squash yields easily when pierced with a fork. This roasting process concentrates the flavors and adds a subtle sweetness.
- Cook the pasta:
- While the vegetables roast, bring a large pot of water to a rolling boil. Add a tablespoon of salt to the water this seasons the pasta from within. Add your pasta and cook until just al dente, about 1 minute less than package directions. The pasta will continue cooking slightly when combined with the hot sauce. Reserve half a cup of pasta water before draining, which can help thin the sauce if needed later.
- Create the roux:
- In a large saucepan over medium heat, melt the butter until it starts to foam but not brown. Add the minced garlic and sauté for exactly one minute, stirring constantly to prevent burning. The garlic should become fragrant but not colored. Sprinkle the flour over the butter and garlic, whisking constantly to prevent lumps. Cook this mixture for 1 to 2 minutes until it smells slightly nutty and turns a light golden color. This step cooks out the raw flour taste.
- Make the béchamel:
- Slowly pour in the milk while whisking vigorously to prevent lumps from forming. Start with just a quarter cup, incorporating completely before adding more. Once all milk is added, bring the mixture to a gentle simmer, stirring frequently with a wooden spoon to prevent scorching on the bottom. Cook for 3 to 4 minutes until the sauce coats the back of a spoon and a finger drawn through leaves a clear path.
- Blend the squash:
- Transfer the roasted squash and onion mixture to a blender. Add about half a cup of the milk mixture to help it blend smoothly. Secure the lid and blend on high speed until completely smooth and velvety, about 1 minute. You should see no flecks of squash remaining. If your blender struggles, add a bit more liquid from the milk mixture.
- Combine the sauce components:
- Pour the vibrant orange squash purée back into the saucepan with the remaining milk mixture. Stir until fully incorporated. Add the nutmeg and smoked paprika, stirring to distribute evenly. Reduce heat to low and add the cheeses one handful at a time, stirring until each addition is fully melted before adding more. This prevents the sauce from becoming grainy. Season with salt and freshly ground black pepper to taste, remembering that the cheese adds saltiness.
- Combine with pasta:
- Add the drained pasta directly to the sauce, folding gently with a rubber spatula to coat every piece evenly. If the sauce seems too thick, add a splash of the reserved pasta water to achieve your desired consistency. The starch in the water helps maintain the sauce's silky texture.
- Add the optional topping:
- For an extra special touch, transfer the mac and cheese to a baking dish. Mix panko breadcrumbs with melted butter until every crumb is moistened. Sprinkle this mixture evenly over the top. Place under the broiler for 2 to 3 minutes, watching carefully, until the top is golden brown and crispy.

The butternut squash is truly the star of this dish. I discovered its magic in mac and cheese after trying to create healthier comfort foods for my family. The first time I served it, no one realized they were eating vegetables until I revealed my secret ingredient. Now it's requested specifically as "the orange mac and cheese" and has become our traditional first-day-of-fall dinner.
Make-Ahead Instructions
This dish works wonderfully as a make-ahead meal. Prepare everything except the breadcrumb topping and store in an airtight container in the refrigerator for up to 3 days. When ready to serve, transfer to a baking dish, add a splash of milk, and heat covered at 350°F for about 20 minutes. Add the breadcrumb topping and broil just before serving. The sauce may thicken considerably when chilled, but gently reheating with additional milk will restore its creamy consistency.
Smart Substitutions
If butternut squash isn't available, sweet potato makes an excellent substitute with a similar color and texture. For a dairy-free version, use unsweetened almond milk and your favorite plant-based cheese substitutes, though you may need to add a tablespoon of nutritional yeast to enhance the cheesy flavor. Gluten-free pasta and a one-to-one gluten-free flour blend work perfectly for those with gluten sensitivities. For a protein boost, stir in 2 cups of shredded rotisserie chicken or 1 cup of white beans before the final bake.
Seasonal Adaptations
In summer, replace butternut squash with yellow summer squash or sweet corn puree for a lighter version. Spring calls for the addition of fresh peas and asparagus tips folded in at the last minute. Winter variations benefit from roasted garlic instead of fresh and a pinch of cayenne for extra warmth. For special occasions in any season, consider folding in sautéed mushrooms and truffle oil for an elegant twist on this humble comfort food.
Additional Section 3
Fresh herbs like sage or thyme can be added to the squash while roasting for seasonal flair. Adding roasted Brussels sprouts or crispy bacon takes this from side dish to main course. For holiday gatherings, transfer to individual ramekins for an elegant presentation.

Taste and adjust seasonings as needed before serving. This mac and cheese is best enjoyed immediately for optimal texture, but leftovers can be reheated gently.
Recipe FAQ Section
- → How can I make the sauce extra creamy?
Use whole milk, plenty of shredded cheddar, and blend the roasted squash thoroughly for the smoothest texture.
- → Is the panko topping necessary?
The panko topping adds crunch but can be skipped or replaced with gluten-free breadcrumbs for a softer finish.
- → Can I use pre-cut squash?
Yes, pre-cut squash works well and saves prep time. Roast as directed until tender and slightly caramelized.
- → Which pasta shapes are best?
Elbow macaroni, shells, or rotini are great options as they hold the creamy sauce effectively.
- → How do I store leftovers?
Refrigerate in an airtight container for up to 3 days. Reheat gently on the stove or in the microwave with a splash of milk.
- → Can I make this dairy-free?
Yes, substitute plant-based milk and cheese alternatives to suit dairy-free needs; adjust seasonings to taste.