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Baked Butternut Squash Mac and Cheese

Plated portion of butternut squash mac and cheese showing creamy sauce and toasted crumbs.
This baked butternut squash mac and cheese is everything you love about the classic, creamy sauce, gooey cheese, and a golden breadcrumb crust, with a cozy touch. The butternut squash purée adds warmth and depth, making it a perfect vegetarian dinner for weeknights, holidays, or anytime you’re craving real homemade comfort food.
Prep Time 20 minutes
Cook Time 45 minutes
Total Time 1 hour 5 minutes
Serving Size 6

Equipment

  • Large pot
  • Steamer basket or colander
  • Blender or food processor
  • Baking dish 9x13-inch
  • Wooden spoon

Ingredients

For the Pasta and Sauce

  • 12 ounces elbow macaroni about 4 cups uncooked
  • 2 ½ cups butternut squash peeled and cut into 1-inch cubes
  • 2 tablespoons unsalted butter
  • 1 ½ cups milk whole milk preferred
  • Salt and pepper to taste
  • ½ teaspoon ground nutmeg
  • ½ teaspoon smoked paprika optional, for color
  • 2 cups sharp cheddar cheese shredded
  • ½ cup mozzarella shredded
  • ½ cup Parmesan cheese grated

For the Topping

  • ½ cup breadcrumbs plain or panko
  • Salt and pepper to taste
  • 1 tablespoon butter melted
  • 1 teaspoon fresh thyme finely chopped

Instructions

  • Add diced squash to a steamer basket set over simmering water. Cover and steam for 10-12 minutes, or until fork-tender.
  • Meanwhile, bring a large pot of salted water to a boil. Cook the macaroni 1 minute less than the package directions for an al dente texture. Drain and set aside.
  • In a blender or food processor, combine the steamed squash, milk, melted butter, salt, pepper, nutmeg, and paprika. Blend until smooth and creamy.
  • Pour the blended sauce into a large pot (you can reuse the pasta pot after draining). Set over medium-low heat and whisk in cheddar, mozzarella, and Parmesan until melted and smooth.
  • Add the drained pasta to the sauce and stir until evenly coated. The mixture should be rich, creamy, and thick.
  • Transfer the mac and cheese to a 9x13-inch baking dish. In a small bowl, combine breadcrumbs, melted butter, salt, pepper, and thyme. Sprinkle evenly over the top.
  • Bake at 375℉ for 20-25 minutes, until bubbling around the edges and the topping is crisp and golden. Let rest for 5 minutes before serving.

Notes

  • Use frozen butternut squash cubes to save prep time. Just steam directly from frozen.
  • Stir in ¼ cup cream cheese with the cheddar for a richer sauce.
  • For a shortcut, skip baking and serve straight from the stovetop as creamy mac and cheese.
  • Leftovers keep 3-4 days in the fridge and reheat best in the oven at 350°F (covered) for 10-15 minutes.
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