Creamy Butternut Squash Macaroni and Cheese Recipe

This butternut squash mac and cheese features a silky roasted butternut squash cheese sauce blended smooth with garlic and onion, paired with sage-infused pasta and a savory breadcrumb topping for a crunchy finish. It bakes in a casserole dish and works well as a comforting main or a festive side.

If you love both cheese and fall flavors, this recipe combines the best of both worlds. Roasting the butternut squash brings a richer, deeper sweetness than steaming, and roasting the onion and garlic alongside the squash adds savory complexity. The sauce is blended with milk and reserved pasta water for the ideal creamy texture.

Ingredients Needed for Baked Butternut Squash Mac and Cheese

The recipe breaks down into three main components: the butternut squash cheese sauce, the sage-flavored pasta, and the breadcrumb topping.

• Sauce: Roasted butternut squash combined with roasted onion and garlic, blended with 2% milk, reserved pasta water, and shredded cheeses to create a smooth, creamy sauce.
• Breadcrumb topping: Plain breadcrumbs toasted with herbs and spices to add a crunchy, savory finish.
• Pasta: Pasta cooked just shy of al dente in a mix of broth and water with fresh sage and a touch of ground cloves so the noodles absorb extra flavor before baking.

Easy Substitutions & Variations

• Pasta: Cavatappi is ideal for trapping sauce, but rigatoni, penne or fusilli work equally well.
• Cheese: Use mostly cheddar for flavor; you can substitute part of the blend with Gruyère, Colby Jack, or other melty cheeses you prefer.
• Swap the squash: Pumpkin or sweet potato can replace butternut squash for a similar sweet-savory profile.
• Add protein: Fold in cooked shredded chicken or cubed roasted chicken to make a heartier, protein-rich meal.

More Mac and Cheese Ideas

• Classic baked mac and cheese for a timeless side
• Protein-packed options like Instant Pot mac and cheese
• Creative variations such as avocado mac and cheese or cauliflower chicken mac
• Vegan versions that swap dairy for plant-based alternatives

Storage Instructions

Store leftovers in an airtight container in the refrigerator for 3–5 days. For longer storage, the casserole can be frozen in a suitable freezer-safe container for up to 2 months; thaw in the refrigerator overnight before reheating.

Reheating Mac and Cheese

When reheating, add a small amount of milk to restore creaminess and prevent the sauce from separating. Reheat gently to preserve texture.

Oven Method

Preheat the oven to 350°F. Place mac and cheese in an oven-safe dish, stir in 1–2 tablespoons of milk (adjust as needed), cover with foil, and warm for 10–20 minutes depending on portion size. Remove foil and bake a few extra minutes if you want the top crispier.

How to Serve

This mac and cheese makes a delightful holiday side for Thanksgiving or other gatherings, but it’s hearty enough to serve as a main. Garnish with freshly chopped sage for a bright, herbal finish. Pair with roasted or pan-seared chicken, grilled steak, or a crisp green salad for a balanced meal.

Butternut Squash Mac and Cheese Recipe

Summary: Roasted butternut squash blended with roasted onion and garlic makes a rich, slightly sweet cheese sauce that coats sage-infused pasta. Topped with toasted breadcrumbs, this baked casserole is creamy, flavorful, and crowd-pleasing.

Recipe Details

• Prep time: 20 mins
• Cook time: 45 mins
• Total time: 1 hr 5 mins
• Servings: 8

Ingredients

Butternut Squash Cheese Sauce

• 1/2 large butternut squash, seeded and quartered (about 3 cups puree)
• 3/4 teaspoon salt, divided
• 1/4 teaspoon cayenne pepper
• 1/4 teaspoon ground black pepper
• 2 tablespoons olive oil, divided
• 1/2 large white onion, diced
• 4 garlic cloves, peeled
• 1 cup 2% milk
• 2 cups reserved pasta water (amount may vary)
• 2 cups shredded cheddar cheese
• 2 cups shredded mozzarella (or Italian blend)

Pasta

• 4 cups broth (any kind)
• 4 cups water
• 6 fresh sage leaves
• 1 teaspoon salt
• 1/4 teaspoon ground cloves
• 16 oz cavatappi or other pasta

Breadcrumb Topping

• 1 cup plain breadcrumbs
• 1 teaspoon salt
• 1/4 teaspoon pepper
• 1 teaspoon dried sage
• 1 teaspoon dried thyme
• 1 teaspoon garlic powder

Instructions

1. Preheat the oven to 400°F and prepare a baking sheet with nonstick spray.
2. Mix 1/2 teaspoon salt with the cayenne and black pepper in a small bowl. Drizzle 1 tablespoon olive oil over the butternut squash quarters, season with the spice mix, and rub to coat. Arrange squash to one side of the baking sheet.
3. On the other side, place the diced onion and whole garlic cloves. Drizzle with the remaining tablespoon of olive oil and sprinkle with the remaining 1/4 teaspoon salt.
4. Roast for 20 minutes, then remove the onions and garlic to prevent burning. Flip the squash and roast an additional 20–30 minutes, until fork-tender.
5. While the squash roasts, bring broth, water, sage leaves, 1 teaspoon salt and ground cloves to a boil in a large pot. Add pasta and cook until just under al dente. Reserve 2 cups of pasta water, discard the sage leaves, then drain and rinse the pasta with cold water to stop cooking.
6. Toast the breadcrumb topping: heat a small skillet over medium heat, combine breadcrumbs with salt, pepper, dried sage, thyme and garlic powder, and toast until golden, about 4–5 minutes. Set aside.
7. When the squash is done, let it cool slightly, then peel away the skin. Add the roasted squash flesh, roasted onion, garlic, and 1 cup reserved pasta water to a high-speed blender. Blend until smooth.
8. Add the cheddar to the blender and blend until melted, then add the mozzarella or Italian cheese blend and blend until smooth and combined. Stir in 2% milk and blend to reach a thick, creamy consistency. If the sauce is too thick, thin with additional pasta water by the tablespoon.
9. Switch the oven to broil. Spray a 9×13 inch casserole dish with cooking spray. Add the pasta, pour the squash cheese sauce over the noodles and stir to combine. Sprinkle the toasted breadcrumb topping evenly over the top.
10. Broil 2–3 minutes until the topping is golden and crisp. Remove from the oven and garnish with freshly chopped sage before serving.

Tips & Notes

• Remove the onion and garlic halfway through roasting to avoid burning and to preserve sweetness.
• Adjust sauce thickness with reserved pasta water; add a tablespoon at a time until the desired consistency is reached.
• This dish reheats well when covered and warmed gently with a splash of milk to restore creaminess.

Nutrition (approx.)

Per serving: Calories 445; Carbohydrates 55 g; Protein 20 g; Fat 18 g; Fiber 5 g; Sugar 8 g. Nutrition is an estimate and should be used as an approximation.