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close up view of butternut squash mac and cheese being scooped from baking dish

Gluten-free Baked Butternut Squash Mac and Cheese

This gluten-free baked butternut squash mac and cheese is light and creamy. The butternut squash gives it a ton of flavor and creaminess and a little bit of cheese keeps it nice and light.
Course Main Course, Side Dish
Cuisine American, Italian
Keyword butternut squash, macaroni, macaroni and cheese
Prep Time 35 minutes
Cook Time 30 minutes
Servings 8 side servings
Calories 619kcal


Ingredients for Macaroni and Cheese

  • 2-2 1/2 lb. butternut squash, peeled and cubed (about 4 cups cubed)
  • 1 tbsp. extra-virgin olive oil or avocado oil
  • 16 oz gluten-free penne noodles (see notes)
  • 2 1/2 cups whole milk, divided
  • 8 oz sharp white cheddar cheese, shredded (see notes)
  • 4 oz Parmigiano Reggiano, shredded
  • 1 tsp. onion powder
  • 1/2 tsp. fine sea salt

Ingredients for Crumb Topping

  • 1/2 cup almond flour
  • 1 tbsp. extra-virgin olive oil
  • 1/4 cup chopped, fresh sage


  • Preheat oven to 350.
  • Toss cubed butternut squash in 1 tablespoon of oil and spread out squash on a baking sheet. Bake squash for 20-25 minutes, or until you can easily pierce the squash cubes with a fork.
  • While the squash is baking, using a large stock pot, cook the pasta according to package and set aside.
  • Add the cooked squash and 1/2 cup milk to a high-speed blender. Blend on med/med-high until all squash is pureed. Scrape down sides if needed.
  • In a large stock pot (you can use the one you cooked the noodles in) add in the remaining 2 cups of milk and shredded cheeses. Stir continuously until all cheese is melted. Add in the pureed butternut squash, onion powder, and salt. Mix until combined.
  • Add cooked noodles back to pot with the butternut squash and cheese. Mix until combined and then pour into a 2-2.5 qt. baking dish or 9x11 glass baking pan.
  • In a separate bowl, combine the almond flour, 1 tbsp. oil extra-virgin olive oil, and chopped sage. Sprinkle over macaroni.
  • Bake uncovered at 350 for 20-25 minutes, or until completely heated through. Sprinkle with additional fresh sage if you have some left over.
  • Enjoy!


  • Make sure to buy block cheese and shred the cheese yourself. Pre-shredded cheese won't melt as well and won't turn out the same in this recipe. 
  • Don't overcook the noodles. They will continue to cook when you bake the mac and cheese. They can even be slightly underdone after you boil them (but not crunchy still). 
  • I prefer Penne noodles, but any tube shaped noodle will work. If not gluten-free, look for whole wheat noodles (it's a whole grain, so keeps it a real food). 


Calories: 619kcal | Carbohydrates: 68g | Protein: 25g | Fat: 28g | Saturated Fat: 14g | Cholesterol: 59mg | Sodium: 605mg | Potassium: 783mg | Fiber: 6g | Sugar: 9g | Vitamin A: 15725IU | Vitamin C: 30mg | Calcium: 574mg | Iron: 3mg