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Gluten Free Mac and Cheese Recipe

Butternut Squash Mac and Cheese

Butternut Squash Mac and Cheese is a fun spin on an American classic dish. Using the butternut squash makes the recipe incredibly creamy. 
Course Dinner
Cuisine American, Vegetarian
Keyword butternut squash, pasta
Prep Time 30 minutes
Cook Time 1 hour
Total Time 1 hour 30 minutes
Servings 12 people
Calories 378kcal
Author Maike


Roasting the Butternut Squash

Making the Pasta

  • 12 ounces elbow pasta gluten-free
  • ½ tablespoons olive oil
  • 1 teaspoons salt

Making the Cheese Sauce

  • ½ cup all-purpose flour (gluten-free) millet or almond flour will work too
  • 4-6 tablespoons unsalted butter
  • 4 cups milk
  • 12 ounces shredded Cheddar cheese I used sharp
  • 1 cup vegetable broth
  • 1 tablespoons dry mustard


  • Cook your gluten free pasta according to the instructions, BUT SUBTRACT 3 minutes from the recommended boiling time. This will prevent the pasta from becoming mushy later. Add ½ tablespoon of olive oil to keep the pasta from sticking together. Rinse pasta and set aside. 

Making Butternut Squash Puree

  • Preheat the oven to 400°. Line a large baking sheet with aluminum foil.
  • Put the diced butternut squash in a large bowl and add olive oil, salt, pepper, and nutmeg. Toss and make sure the pieces are evenly coated. Next transfer the butternut squash onto a baking sheet and roast 25-30 minutes.
    Once you've removed the roasted butternut squash reduce the heat to 350°.
  • Once the butternut squash is soft, take it out of the oven and transfer it into a food processor. Add ½ cup of vegetable broth to the food processor. Blend until the butternut squash turns into puree. Set aside.

Making the Cheese Sauce

  • In a large sauté pan (or Dutch oven) melt your butter over medium-low heat, add the gluten free flour and stir constantly until the butter and flour have created a paste (roux).
  • Now slowly pour the milk into the mixture. Stir frequently until the milk has warmed and the mixture has thickened (about 7-10 minutes) Then it's time to add salt, pepper, and dry mustard to the mix. Add ¾ of the shredded Cheddar to the sauce. and simmer for a couple of minutes. 
  • Take the cheese sauce off the stove and add the cooked pasta to the mixture. Now transfer everything into a large rectangular baking dish. Top with the remaining shredded cheese. 
  • Transfer the casserole dish to the oven and cook for 20 minutes. Next set your oven to broil and broil for about 5 minutes or until you see a nice brown crust. ~ Time to enjoy.


Calories: 378kcal | Carbohydrates: 38g | Protein: 14g | Fat: 20g | Saturated Fat: 11g | Cholesterol: 48mg | Sodium: 735mg | Potassium: 406mg | Fiber: 3g | Sugar: 6g | Vitamin A: 8631IU | Vitamin C: 16mg | Calcium: 339mg | Iron: 1mg