Let’s bring cozy fall flavors to our favorite comfort food with this Butternut Squash Mac and Cheese. This healthier mac and cheese is extra creamy and seasoned with fresh sage and a pinch of nutmeg.

serving spoon filled with butternut squash mac and cheese held over dish

As soon as the weather begins to turn cool in the fall, I start dreaming of my favorite butternut squash recipes. A bowl of creamy Butternut Squash Soup really hits the spot on a chilly evening, as does a steaming dish of this butternut squash mac and cheese. 

To make this easy macaroni and cheese recipe, you’ll make a puree of cooked butternut squash to stir into the cheese sauce. Butternut squash blends up incredibly smoothly and creates a luxuriously creamy mac and cheese. Since the squash adds creaminess we can use less cheese without sacrificing on texture or flavor. Healthier mac and cheese that’s still so incredibly rich and flavorful? I’ll take it!

I’ve added some fresh sage, sautéed in a little butter with garlic, to this butternut squash mac and cheese because the flavors of sage and butternut pair so well together. The flavor profile reminds me of one of my favorite pasta dishes, butternut squash ravioli. This recipe has all of the same sweet and savory flavors, without the work of filling ravioli. I hope you love it as much as we do!

Butternut Squash Mac and Cheese Ingredients

ingredients for butternut squash mac and cheese recipe

  • Butternut Squash: You’ll need half of a small/medium butternut squash for this recipe. I usually save the other half to make Roasted Butternut Squash to serve with another meal. 
  • Pasta: I like to use medium shell pasta because the shell shape holds extra cheese sauce. Feel free to use another short pasta shape, such as elbow macaroni.
  • Butter & All-Purpose Flour: The butter and flour combine to make a roux, which thickens the macaroni and cheese sauce.
  • Garlic: Fresh minced garlic adds flavor.
  • Fresh Sage Leaves: The flavor of fresh sage pairs especially well with butternut squash. If you don’t have fresh sage you can leave it out or substitute a teaspoon of fresh thyme leaves. Fresh herbs are best in this recipe, and I don’t recommend substituting dried herbs.
  • Salt, Pepper & Nutmeg: To season the sauce. Freshly ground nutmeg is amazing here, but store bought ground nutmeg also works well.
  • Vegetable Broth & Milk: These are used to make the cheese sauce. Using a combination of broth and milk creates a rich sauce that isn’t too heavy.
  • Sharp Cheddar & Sharp White Cheddar Cheese: We loved this combination of cheeses with the butternut squash. Gruyere would also be delicious and could be substituted for either type of cheddar.

Find the full printable recipe with ingredient amounts and instructions in the recipe card below.

How to Make Butternut Squash Mac and Cheese

  1. Cook the butternut squash. You can bake it in the oven, steam it on the stove, or cook the butternut squash in the Instant Pot. The recipe card below includes directions for all three cooking methods. roasted half butternut squash on baking sheet
  2. Put the squash in a blender or food processor, add 1/2 cup of the vegetable broth, and puree until smooth. pureed squash in food processor
  3. Cook the pasta according to the package directions. Drain and return to the empty pot.
  4. In a medium saucepan, melt the butter. Add the garlic and chopped sage. Cook and stir for 1 minute.
  5. Whisk in the flour, nutmeg, salt and pepper. Stir and cook for 30 seconds. flour and seasonings added to saucepan
  6. Whisk in the remaining broth and the milk. Cook until thickened, about 3 minutes. cream sauce in saucepan with whisk
  7. Remove from the heat. Stir in the shredded cheese. stirring shredded cheese into sauce
  8. Stir in the pureed squash mixture. stirring pureed squash into sauce
  9. Stir the butternut cheese sauce into the pasta. Serve and enjoy!stirring squash cheese sauce into pasta shells in pot

Recipe Tips

  • I highly recommend buying blocks of cheese and shredding the cheese yourself using a box grater. The pre-shredded cheese that you buy at the grocery store is often coated with an anti-caking agent that prevents it from melting smoothly.
  • To keep this mac and cheese on the healthier side, I kept the amount of cheese to a minimum. The pureed butternut squash makes the final dish exceptionally creamy, even with less cheese. If you want a lot of cheesy flavor, feel free to increase the amount of white cheddar cheese to 6 ounces. 
  • If the mac and cheese is not hot enough after mixing in the sauce, warm it over low heat on the stove, stirring often, until hot. You might find that it needs to be heated a bit more if the butternut squash was cool by the time it was added to the sauce.
  • Can you use canned butternut squash puree? Fresh butternut squash puree is easy to make and is going to give you the best flavor. If you really want to use canned, you can use about 1 cup of canned squash puree in this recipe. Omit the 1/2 cup of broth that is used when pureeing the squash.
  • To make a bread crumb topping for this recipe: Stir together 3/4 cup breadcrumbs and 1 tablespoon of melted butter. You can also stir in 1/4 cup of grated Parmesan cheese, if desired. Put the macaroni and cheese in a casserole dish, sprinkle on the topping, and bake at 375° F for about 15 minutes, until the topping is golden brown.

two bowls of butternut mac and cheese next to casserole dish

Serving Suggestions

I usually serve this butternut squash mac and cheese as a vegetarian main course for dinner. It also makes a delicious Thanksgiving side dish. If you’re serving this macaroni and cheese as a main dish, side dishes that pair well include Kale Salad, Green Salad, Roasted Broccoli or Roasted Green Beans. My family loves bread, so I often serve either Dinner Rolls, Garlic Bread or Honey Yeast Rolls as well. 

butternut mac and cheese with fresh sage in casserole dish

More Mac and Cheese Recipes

spoonful of butternut mac and cheese held over blue serving dish

Butternut Squash Mac and Cheese

Servings: 8 servings
This Butternut Squash Mac and Cheese is the best cozy fall comfort food. The butternut squash makes it extra creamy and a touch of fresh sage and nutmeg round out the flavors.
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Ingredients

  • 1 pound butternut squash, half of a small/medium squash
  • 16 ounces medium shell pasta, or elbow macaroni pasta
  • 3 tablespoons unsalted butter
  • 1 clove garlic, minced
  • 5 fresh sage leaves, chopped, optional*
  • 3 tablespoons all-purpose flour
  • ½ teaspoon salt
  • ¼ teaspoon pepper
  • â…› teaspoon ground nutmeg
  • 1 cup low sodium vegetable broth, divided, or substitute with milk
  • 1 cup milk
  • 4 ounces sharp white cheddar cheese, shredded
  • 4 ounces sharp cheddar cheese, shredded

Instructions
 

First, cook the butternut squash by following one of the 3 methods below: oven, stove or Instant Pot.

    To Cook Butternut Squash in the Oven

    • Halved Squash: Preheat oven to 375° F. Line a rimmed baking sheet with parchment paper. Slice a small amount off of the stem and base ends of the squash and then cut the squash in half lengthwise. Scoop out the seeds. Place the squash halves, cut side down, on the prepared baking sheet. Roast in the oven for 35-45 minutes, until soft when pierced with a fork. Let cool slightly and then scoop the squash out of the skin.
      Cubed Squash: Bake 1-inch squash cubes at 400° on a parchment paper lined baking sheet for 30-35 minutes, tossing halfway through the cook time, until soft.

    To Steam Butternut Squash on the Stove

    • Put an inch or two of water in the bottom of a pot or saucepan. Add a steamer basket to the pot.
    • Bring to a boil over high heat. Once boiling, add 1-inch squash cubes to the steamer basket and cover the pot. Reduce heat to medium high and cook for 7-9 minutes, until tender.

    To Cook Butternut Squash in the Instant Pot

    • Quartered Butternut Squash: Cut off the stem end of the squash. Cut the squash in half crosswise, at the point where the squash widens. Stand each squash half on its flat end, cut in half, and then scoop out the seeds. Put 1 cup water in the Instant Pot (1½ cups for 8 quart pot). Put the metal trivet in the pot and place the four squash pieces on the trivet. Pressure cook at high pressure for 10 minutes, followed by a 5 minute natural release. Quick release the remaining pressure. Let cool slightly and then scoop squash out of the skin.
      Cubed Squash: Put 1 cup of water in the bottom of the Instant Pot (1½ cups for 8 quart pot). Add a steamer basket to the pot. Put 1-inch squash cubes in the steamer basket. Cook at high pressure for 3 minutes. Quick release the pressure.

    To Make the Butternut Mac and Cheese

    • Place the squash in a blender or food processor and add ½ cup of the vegetable broth. Puree until very smooth. Set aside.
    • Bring a large pot of water to a boil. Cook the pasta according to the package directions. Drain and return pasta to the empty pot.
    • In a medium saucepan, melt the butter over medium heat. Add the garlic and chopped sage and cook for 1 minute, stirring.
    • Whisk in the flour, nutmeg, salt and pepper. Cook for 30 seconds, stirring constantly.
    • Whisk in the remaining ½ cup of broth and the milk. Cook, stirring often, until thickened, about 3 minutes.
    • Remove from the heat and stir in the cheese. Then stir in the pureed squash mixture.
    • Stir the butternut cheese sauce into the pasta.
    • If the mac and cheese is not hot enough (this may be the case if the squash was cooled), warm it over low heat on the stove, stirring often, until hot. Serve.

    Notes

    • Fresh herbs are best in this recipe. 1 teaspoon of fresh thyme can be substituted for the fresh sage, if desired.
    • Do not use store-bought pre-shredded cheese because it is often coated with an anti-caking agent that prevents it from melting smoothly.
    • The pureed butternut squash makes the mac and cheese very creamy, even with less cheese. If you want a lot of cheesy flavor, feel free to increase the amount of white cheddar cheese to 6 ounces. 
    • To make a bread crumb topping for this recipe: Stir together 3/4 cup breadcrumbs and 1 tablespoon of melted butter. You can also stir in 1/4 cup of grated Parmesan cheese, if desired. Put the macaroni and cheese in a casserole dish, sprinkle on the topping, and bake at 375° F for about 15 minutes, until the topping is golden brown.
    • Leftover mac and cheese can be stored in an airtight container in the refrigerator for up to 3 days.
    Calories: 419kcal, Carbohydrates: 53g, Protein: 16g, Fat: 16g, Saturated Fat: 9g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 1g, Cholesterol: 44mg, Sodium: 458mg, Potassium: 401mg, Fiber: 3g, Sugar: 5g, Vitamin A: 6555IU, Vitamin C: 12mg, Calcium: 281mg, Iron: 1mg
    Nutrition information is an estimate.
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