Baked Butternut Squash Macaroni and Cheese

This Baked Butternut Squash Macaroni and Cheese is perfect for holiday parties and any cozy winter meal!

This Baked Butternut Squash Macaroni and Cheese is perfect for holiday parties and any cozy winter meal! Get the recipe from Savory Simple.

The holidays means different things to different people. One of the main focuses for me is the wonderful food. Preparing food is is way for me to express myself to friends and family, and I love sharing the flavors of the season with them.

This baked butternut squash macaroni and cheese is everything I love about the autumn and winter months. It highlights seasonal produce, and it’s cozy, filling, comfort food.

Topping butternut squash mac and cheese with more cheese.A photo of baked butternut squash macaroni and cheese, right out of the oven.

The butternut squash adds subtle sweetness to contrast the earthiness of the sage, the savoriness of the Wisconsin Cheddar, and the saltiness of the Wisconsin Parmesan. It’s a great dish to prepare in advance if you’re entertaining guests, up to 24 hours beforehand. You can build the whole thing and then bake it while serving appetizers.

You can also easily transport it to someone else’s home. Simply follow the recipe as written, but instead of baking it as written in Step 7, wrap the casserole dish in plastic wrap and chill until you’re ready to continue. Then bake according to the instructions in Step 8 for perfect, gooey macaroni and cheese.

Looking for more butternut squash recipes? Check out my Chicken Pot Pie with Butternut Squash and Bacon!

This Baked Butternut Squash Macaroni and Cheese is perfect for holiday parties and any cozy winter meal! Get the recipe from Savory Simple.

Print Pin Recipe

Baked Butternut Squash Macaroni and Cheese

5 from 3 votes
This Baked Butternut Squash Macaroni and Cheese is perfect for holiday parties and any cozy winter meal!
Course Main Course
Cuisine American
Prep Time 20 minutes
Cook Time 1 hour
Total Time 1 hour 20 minutes
Servings 12
Calories 406
Author Jennifer Farley


  • 1 large butternut squash (approximately 2 1/2 pounds), peeled, deseeded and diced
  • 1 tablespoon extra virgin olive oil
  • 3/4 teaspoon kosher salt, divided
  • 1/2 teaspoon ground black pepper, divided
  • 1 pound elbow macaroni
  • 4 ounces shredded Mild Wisconsin Cheddar Cheese
  • 4 ounces shredded Sharp Wisconsin Cheddar Cheese
  • 2 ounces shredded Wisconsin Parmesan Cheese
  • 3 ounces unsalted butter
  • 1 medium yellow onion, finely diced
  • 2 cloves garlic, minced
  • 10 large or 15 small sage leaves, chopped
  • 3/4 cup all-purpose flour
  • 4 cups whole milk (part-skim may be substituted)


  • Preheat the oven to 400 degrees F, and line a large baking sheet with aluminum foil. Set aside 2 cups of the butternut squash, then toss the remaining squash with the olive oil, 1/2 teaspoon salt and 1/4 teaspoon black pepper. Spread evenly on the baking sheet and roast for 20 minutes, stirring once during the process to prevent sticking.
  • While the butternut squash is roasting, steam the reserved squash until fork tender, approximately 10 minutes, then mash and set aside.
  • Prepare the macaroni according to package instructions, then drain and rinse in cold water to prevent sticking. Set aside.
  • Combine the cheddars and parmesan cheese in a medium-sized bowl. Remove 1 cup and set aside.
  • In a large Dutch oven or heavy bottom sauce pot, melt 1 tablespoon of butter over medium-low heat. Add the onions and garlic, cooking and stirring until translucent, approximately 3-5 minutes. Stir in half the sage and cook until fragrant, approximately 30 seconds. Add the remaining butter and melt, then add the flour to form a paste. Using a spatula, stir the paste for approximately 1-2 minutes, then ladle in some of the milk, stirring. Slowly add in the remaining milk, stirring, and turn the heat up to medium-high.
  • Whisk constantly as the sauce heats up and thickens. Once it is thick, remove the sauce from the heat and whisk in the cheese until smooth, omitting the reserved cup. Whisk in the mashed butternut squash and remaining salt and pepper.
  • Combine the macaroni, cheese sauce, and roasted squash, then spread evenly into a 9x13 casserole dish. Top with the reserved cheese and sage. (Note: if you are preparing the dish in advance, cover with plastic wrap and store in the refrigerator until it’s time to cook).
  • Bake in a 350 degrees F oven for 40 minutes, or until the top is melted and the sides are beginning to bubble.


Inspired by a BBC Food recipe


Calories: 406kcal | Carbohydrates: 46g | Protein: 15g | Fat: 17g | Saturated Fat: 10g | Cholesterol: 46mg | Sodium: 379mg | Potassium: 456mg | Fiber: 2g | Sugar: 7g | Vitamin A: 143.6% | Vitamin C: 16.9% | Calcium: 32.8% | Iron: 8.3%

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Disclaimer: This post is sponsored by Wisconsin Cheese. Thank you for supporting the brands that support Savory Simple! 

About Jennifer Farley

Jennifer graduated from the Culinary Arts program at L’Academie de Cuisine, and has worked professionally as a line cook, pastry chef, and cooking instructor. Her cookbook, The Gourmet Kitchen, was published in 2016 by Simon & Schuster.

Affiliate Disclaimer: Posts may contain affiliate links. I am a participant in the rewardStyle and Amazon affiliate programs, which help support Savory Simple by providing me with a small commission fee when you shop through my links, at no additional cost to you.

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