Creamy, cheesy, and SO delicious, this butternut squash mac and cheese is the ultimate fall comfort food. It'll be a hit with the whole family!

Butternut squash mac and cheese! If you thought the Trader Joe’s version was good, you’ll LOVE this homemade one.

I adapted the recipe from my traditional macaroni and cheese. Instead of making a roux with flour and butter, I used pureed roasted squash as the base of the cheese sauce. The squash makes it insanely creamy (even creamier than classic mac!) and adds a subtle sweetness to the rich, cheesy flavor. Bonus: it sneaks in some extra nutrients too!

This butternut squash mac and cheese has been a huge hit in our house. It’s comforting, delicious, and—thanks to the squash—just perfect for fall. I can’t wait for you to try it!

Butternut Squash Mac and Cheese Ingredients

Here’s what you’ll need to make this butternut squash mac and cheese recipe:

Butternut squash, of course! Look for one on the larger side. You’ll need 2 cups of soft roasted squash to make the creamy sauce.
Pasta – Shells are my shape of choice, but elbow macaroni or pipe rigate would work well too.
Three types of cheese – Gruyere, sharp cheddar, and pecorino or Parmesan! The nutty Gruyere and tangy cheddar melt beautifully into the creamy sauce. A little pecorino adds savory depth of flavor.
Shallots – You’ll roast them alongside the squash to add oniony flavor to the sauce.
Extra-virgin olive oil – It helps the squash blend into a creamy puree.
Balsamic vinegar, nutmeg, and ground sage – For fall flavor! The tangy vinegar and warm, earthy seasonings bring out the butternut squash taste.
Onion powder and garlic powder – For an umami kick.
Unsweetened almond milk – Feel free to use 2% or whole milk if you prefer.
Panko breadcrumbs – They create a delicious crispy topping for the comforting pasta.
And salt and pepper – To make all the flavors pop!

Find the complete recipe with measurements below.

How to Make Butternut Squash Mac and Cheese

You can find the full recipe with measurements and step-by-step instructions at the bottom of this post. But to get you started, here’s a quick overview of how it goes:

Start by roasting the squash and shallots.

Tip: To get ahead, do this step in advance. You can store the roasted vegetables in an airtight container in the fridge for up to 4 days or freeze them for up to 3 months. Once they’re cooked, the rest of the recipe comes together quickly!

Meanwhile, prepare the topping by tossing the panko with a little olive oil, and cook the pasta. Before you drain the pasta, reserve 1 1/2 cups of the starchy cooking water.

Next, make the squash puree. Measure 2 cups of the soft roasted butternut squash flesh. Add it to a blender with the shallots, olive oil, balsamic, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper.

Pour in the reserved pasta water…

…and blend until creamy.

Then, make the cheese sauce. Return the pasta pot to the stove, add the almond milk, and warm it over medium heat. Pour in the squash puree and cook, stirring often, until warmed through.

Whisking constantly, gradually add the cheeses, making sure each addition melts fully before adding the next.

Recipe Tip

Grate the cheese yourself! Store-bought shredded cheese is often coated in anti-caking agents, which can prevent it from melting into a smooth and creamy sauce.

When all the cheese is melted and the sauce is creamy, add the cooked pasta. Stir to coat it in the luscious sauce.

Yum!!

Finally, bake the butternut mac and cheese. Transfer it to an oiled 9×13-inch or similar baking dish, and top with the panko. Broil until the topping is crisp and browned.

Let stand for 15 minutes before serving. Then, dig in!

Serving Suggestions

This butternut squash mac and cheese is such a cozy fall dinner! Pair it with a simple veggie side dish like steamed broccoli, roasted broccoli, or roasted Brussels sprouts. It also goes nicely with a fresh salad like one of these:

Another option: Serve the butternut mac and cheese as a Thanksgiving side dish! It’ll be a total crowd-pleaser.

More Recipes You’ll Love

If you love this butternut squash mac and cheese, try one of these Love & Lemons recipes next:

Butternut Squash Mac and Cheese

rate this recipe:

4.92 from 46 votes

Prep Time: 20

Cook Time: 1

Total Time: 1 20

Serves 8

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Creamy, cheesy, and SO delicious, this butternut squash mac and cheese is the ultimate fall comfort food. To get ahead, roast the squash and shallots up to 4 days in advance. Store them in an airtight container in the fridge until you're ready to make the pasta.

Equipment

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 9x13-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.

Notes

*To make this recipe gluten-free, use gluten-free pasta and gluten-free panko.

For a similar vegan recipe, I recommend making my creamy butternut squash pasta or vegan mac and cheese.