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Easy Butternut Squash Baked Mac and Cheese

Silky smooth butternut squash cheese squash generously coats macaroni and is topped with breadcrumbs and more cheese. Kid friendly, easy to make gluten free and great for potlucks and family dinners!
Course Side Dish
Cuisine American
Diet Gluten Free
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Servings 8
Calories 440kcal
Author Lauren


  • 12 ounces elbow macaroni or cavatapi*
  • Salt
  • 1 tablespoon extra-virgin olive oil
  • ½ medium onion ,diced
  • 1 tablespoons fresh thyme leaves + more for garnish
  • 2 cloves garlic ,minced
  • 2 cups chicken stock
  • 10 ounces butternut squash ,peeled and cut into ½-inch cubes
  • 2 tablespoons butter
  • 3 tablespoons all-purpose flour*
  • 2 cups chicken stock
  • 10 ounces butternut squash ,peeled
  • 1 cup cream or half-and-half
  • 2 cups 8 ounces sharp Cheddar, grated
  • ½ cup Gruyere or Swiss Cheese , grated
  • Salt and Pepper
  • Pinch of nutmeg


  • ½ cup panko breadcrumbs*
  • 2 tablespoon grated parmesan optional


  • Preheat the oven to 400˚F. Heat a stock pot filled halfway with water to boil for the pasta.
  • While the water comes to a boil, heat oil in a medium lidded pot over medium heat. Add the onion and sauté over medium heat until tender with golden edges, about 5-7 minutes.
  • Add the garlic and thyme to the onions and stir continuously until fragrant, about 60 seconds. Pour the stock and butternut squash into the pot with the onions; Cover and reduce the heat to a simmer.
  • Pour the pasta into the boiling water with a generous sprinkling of salt and cook both the pasta and squash around 8-11 minutes or until the pasta is al dente or a little over. Drain the pasta, rinse with cold water and return to stock pot off any heat. Carefully, pour the squash and broth mixture into a blender and puree for 40-60 seconds or until completely smooth.
  • In the same medium pan, melt the butter over medium-low heat. Once melted, whisk in the flour until it resembles a paste, then quickly add the butternut puree and half and half. Whisk until the outside of the pan bubbles, then turn off the heat. Add cheddar and swiss and continue whisking until smooth. Add salt, pepper and nutmeg to taste.
  • Pour the sauce over the noodles and stir to coat evenly. Pour into a 9x9" pan. Add breadcrumbs to a small skillet, stirring occasionally over medium heat and until they are golden brown. Evenly sprinkle the breadcrumbs over the top of the macaroni as well as the parmesan. Place about 2 inches under the oven burner and cooke for 10 minutes or until the top is just golden. Serve immediately.


*Gluten free versions of these can easily be subbed to suite a gluten free diet. 


Calories: 440kcal | Carbohydrates: 49g | Protein: 17g | Fat: 20g | Saturated Fat: 11g | Monounsaturated Fat: 2g | Cholesterol: 55mg | Sodium: 972mg | Potassium: 191mg | Fiber: 3g | Sugar: 5g | Vitamin A: 4350IU | Vitamin C: 12.4mg | Calcium: 320mg | Iron: 2mg