Butternut Squash Mac and Cheese

This luxurious take on baked mac and cheese is our go-to make-ahead meal in the fall.

By

Genevieve Yam

Senior Editor

After graduating from the International Culinary Center, Genevieve cooked at Blue Hill at Stone Barns and Per Se. Prior to joining Serious Eats, she was an editor at Epicurious. She grew up between Toronto and Hong Kong and is a graduate of the University of St Andrews in Scotland. She currently lives in New York with her husband and two cats.

Published October 31, 2025

Serious Eats / Robby Lozano

Why It Works

• Folding a blend of fontina, extra-sharp cheddar, and Gruyère into creamy béchamel sauce results in a rich, deeply flavored mac and cheese with a touch of nuttiness.
• Topping the mac and cheese with buttery panko breadcrumbs before baking gives it a satisfying crunch.

I always keep a box of pasta in my pantry and several kinds of cheeses in my fridge. That means that when I have no idea what to make for dinner, I usually end up making mac and cheese. When I’m short on time, it’s former culinary director Kenji’s three-ingredient stovetop mac and cheese, which is simple, satisfying, and takes just 10 minutes to whip up. But when I have the luxury of time and want to go all out—whether for my own family or for a holiday party—I’ll prepare a rich, creamy baked macaroni and cheese, complete with a crispy, buttery breadcrumb topping. Recently, my Birmingham, Alabama-based test kitchen colleague Julia Levy inspired me to try something different: a luxurious autumnal take on baked mac with butternut squash mixed right in with the pasta.

Serious Eats / Robby Lozano

In addition to baked and then puréed butternut squash, Julia’s recipe calls for not one but three different kinds of cheese: fontina, extra-sharp cheddar, and Gruyère. Each cheese plays a role—the fontina adds silkiness, the cheddar a wonderful tanginess, and the Gruyère its signature nuttiness—and they work together to complement the naturally sweet and earthy flavors of the butternut squash. Before being baked, the casserole is topped with buttery sage breadcrumbs for a crispy topping that tastes and smells like the holidays. The result? A delicious, comforting casserole that my friends and family are already requesting on repeat. And even more great news: The casserole can be prepped and refrigerated or frozen days (or months) in advance, making it perfect for getting ahead on holiday cooking.

6 Keys to Making the Best Butternut Squash Mac and Cheese

1. **Use ripe butternut squash. **For the sweetest flavor, reach for a ripe gourd. Unfortunately, you can’t tell a squash’s ripeness by touch, but it should feel heavy for its size and sound hollow when tapped with your knuckles—and when you cut into the squash, the flesh should be a deep orange color.
2. **For easier slicing, microwave your squash first. **Butternut squash can be large and unwieldy. To make it easier to halve, use a fork or sharp paring knife to poke holes all over—then place the gourd on a large plate and microwave on high until just tender enough to cut through easily, three to five minutes. Once it’s cool enough to handle, you can slide your knife right in to halve the squash.
3. For the creamiest mac and cheese, use a béchamel sauce as your base. As our editorial director Daniel wrote in his béchamel recipe, this luscious French sauce is basically “just milk that’s been thickened with a roux made from roughly equal parts of butter and flour,” with a touch of salt, black pepper, and grated nutmeg stirred in. As fancy as the sauce sounds, it’s very simple to prepare: Make the roux by whisking flour into melted butter, then slowly and gradually add your milk. Simmer until thickened, season to taste, and that’s all there is to it.
4. Add a touch of mustard. To cut through the richness of the cheese and provide a balanced flavor, we incorporate a touch of Dijon mustard, which gives the pasta a nice sharpness.
5. Go all out on the cheese. We originally started with fontina and extra-sharp cheddar, but felt that the mac and cheese needed additional oomph. Though we were worried that Gruyère would make the casserole slightly too funky (if that’s really possible), it gave the pasta a pleasant nuttiness that complemented the squash’s sweet and earthy flavor, taking it from “great” to “holy cow, this is awesome,” according to one taster. Have a favorite cheese you want to use? Feel free to use it in place of any of the cheeses—just make sure it’s a semidry cheese like Swiss, Comté, or emmentaler. Avoid moisture-heavy cheeses, such as fresh mozzarella or goat cheese, which may result in a waterlogged casserole.
6. Top it with a buttery panko mixture. Mac and cheese is delicious on its own, but it’s even better when you garnish it with a topping of herby panko breadcrumbs tossed in butter. As the casserole bakes, the breadcrumbs become golden brown and crisp, giving each bite a satisfying crunch.

Editor’s Note

The recipe was developed by Julia Levy; the headnote was written by Genevieve Yam.

Keep Screen Awake

One 2- to 2 3/4 pound (960g) butternut squash, halved and seeded

1 tablespoon (15ml) extra virgin olive oil

1 3/4 teaspoon Diamond Crystal kosher salt, divided; for table salt, use half as much by volume

4 medium garlic cloves (20g), peeled and smashed

1 pound (454g) medium-size pasta shells or other short pasta

6 tablespoons unsalted butter (about 3 ounces; 84g), divided, plus more for greasing

1/4 cup all-purpose flour (about 1 ounce; 32g)

1 teaspoon paprika

1/2 teaspoon freshly ground black pepper

1/4 teaspoon ground nutmeg

2 1/2 cups (590ml) whole milk

1 1/2 cups (355ml) half and half

1 1/2 tablespoons Dijon mustard

12 ounces fontina cheese (340g; about 3 cups), shredded

12 ounces extra-sharp cheddar (340g; about 3 cups), shredded

8 ounces Gruyère cheese (226g; about 2 cups), shredded

1 cup panko breadcrumbs (2 1/2 ounces; 71g)

1 tablespoon minced fresh sage

Adjust oven rack to middle position and preheat oven to 400°F (205ºC). Line a 13- by 18-inch rimmed baking sheet with foil or parchment. Set aside.

Serious Eats / Robby Lozano 1.

Rub oil and 1/2 teaspoon of the salt all over cut sides of butternut squash. Place two smashed garlic cloves in each squash cavity and place squash halves cut side down on prepared baking sheet. Bake until easily pierced with a fork, 30 to 40 minutes. Remove from oven and let cool slightly, about 5 minutes. Reduce oven temperature to 350°F (175ºC) and, using oven mitts, carefully move rack to top third position.

Serious Eats / Robby Lozano 1.

While butternut squash bakes, bring a large pot of lightly salted water to a boil. Add pasta and cook, stirring, until just shy of al dente, about 2 minutes less than cooking time indicated on package. Drain pasta and set aside.

Serious Eats / Robby Lozano 1.

In the now-empty pot, melt 4 tablespoons butter over medium heat. Once melted, add flour, paprika, pepper, and nutmeg, and whisk to form a paste. Continue to cook, whisking constantly, until raw flour scent is gone, about 1 minute. In a 4-cup measuring cup, combine whole milk and half-and-half. Slowly pour milk and half-and-half in a thin, steady stream, whisking constantly and thoroughly and getting into all corners of the saucepan to maintain a homogeneous texture. Sauce will initially become very thick, then get very thin once all the milk is added. Whisk in Dijon to combine.

Serious Eats / Robby Lozano 1.

Scoop out roasted squash flesh (about 3 to 4 cups) and garlic and add to milk mixture in pot. Using an immersion blender, blend squashand garlic into milk mixture until smooth (alternatively, combine squash flesh, garlic, and 2 cups of the milk mixture in a blender; blend until smooth. Stir back to saucepan); bring to a simmer over medium heat. Remove from heat and gradually whisk in fontina and cheddar, about 1/2 cup at a time, until smooth and creamy, 5 to 7 minutes.

Serious Eats / Robby Lozano 1.

Fold in cooked pasta to fully coat in sauce, followed by Gruyère and 1 teaspoon salt. Lightly grease a 9- by 13-inch baking dish with butter and scrape pasta mixture into prepared dish and smooth surface into an even layer.

Serious Eats / Robby Lozano 1.

Microwave remaining 2 tablespoons butter in a medium microwave-safe bowl on low power until melted, about 20 seconds on medium power. Add panko, sage, and remaining 1/4 teaspoon salt, stirring to evenly coat breadcrumb mixture in butter. Scatter panko all over surface of mac and cheese in an even layer. Place baking dish on a 13- by 18-inch rimmed baking sheet and bake at 350ºF on upper-middle rack until browned and bubbling, 35 to 40 minutes. (Ovens can vary; check often to prevent top from burning.)

Serious Eats / Robby Lozano 1.

Remove from oven and let cool for 15 minutes. Serve.

Serious Eats / Robby Lozano

Special Equipment

13- by 18-inch rimmed baking sheet, immersion blender, 9- by 13-inch baking dish

Notes

To make the squash easier to cut, use a fork or sharp paring knife to poke holes all over the gourd. Place on a large plate and microwave on high for 3 to 5 minutes. Once it’s cooled enough to handle, you can slide your knife in easily to halve the squash.

Any semi-firm cheeses, such as cheddar, Swiss, Comté, emmentaler, Gruyère, fontina, or Monterey Jack will work here.

Make-Ahead and Storage

Butternut squash can be roasted, scooped out, and refrigerated in an airtight container for up to 3 days before blending into the cheese sauce.

Mac and cheese can be assembled through the end of step 5, then covered and refrigerated for up to 5 days before baking. Increase baking time by 15 minutes if refrigerating.

If you are planning to freeze the butternut squash mac and cheese, we recommend baking it in a disposable aluminum baking pan. Once cooled, mac and cheese can be wrapped in 1 layer of aluminum foil then tightly wrapped in plastic wrap and frozen for up to 3 months. Thaw overnight in the fridge before baking. Bake in an oven preheated to 350ºF (175ºC) until warmed through.

Nutrition Facts (per serving)
786	Calories
51g	Fat
46g	Carbs
38g	Protein

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Nutrition Facts Servings: 8 Amount per serving Calories 786 % Daily Value* 51g 65% Saturated Fat 29g 145% 153mg 51% 1298mg 56% 46g 17% Dietary Fiber 6g 20% Total Sugars 8g 38g Vitamin C 19mg 93% Calcium 989mg 76% Iron 2mg 14% Potassium 594mg 13% *The % Daily Value (DV) tells you how much a nutrient in a food serving contributes to a daily diet. 2,000 calories a day is used for general nutrition advice.

(Nutrition information is calculated using an ingredient database and should be considered an estimate.)