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mac and cheese cooked and served in an aqua color bowl

Butternut Squash Macaroni and Cheese

This Butternut Squash Mac and Cheese is so creamy and comforting with healthy squash that's made on the stovetop!
5 from 1 vote
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Course: Main Course
Cuisine: American
Prep Time: 15 minutes
Cook Time: 15 minutes
Servings: 6
Calories: 260kcal


Butternut Squash Puree

  • 1 large butternut squash peeled, seeded, and cut into 1/2 inch cubes - or 1 (15-ounce bag) frozen cubed butternut squash (do not thaw)
  • 1 1/2 cups water
  • 1 1/2 tablespoons finely chopped sage - can also use dried spice
  • 1 1/2 tablespoons fresh thyme sprigs - can also use dried spice
  • 1 cup vegetable broth - or chicken broth
  • 1 teaspoon Kosher salt
  • 1 teaspoon pepper

Butternut Squash Macaroni and Cheese

  • 1 tablespoon ghee - or butter
  • 1 tablespoon tapioca starch - can also use arrowroot, cornstarch or flour
  • 3 cloves garlic, minced
  • 1 1/2 cups almond milk - any milk is fine
  • 1 tablespoon Dijon mustard
  • 1 1lb macaroni of choice, cooked to package directions - can also use rigatoni or penne pasta
  • 1 1/2 cups grated sharp cheddar cheese - about 6 ounces
  • 1/4 cup finely grated Parmesan cheese - plus more for garnish


  • To a large pot, cover cubed butternut squash (fresh or frozen) with 1 1/2 cup water. Simmer over medium heat, until squash is tender about 10-15 minutes. (If using frozen squash, it will be tender at about 10 minutes, if fresh, it will be tender closer to 15 minutes. Do not overcook). Turn off the heat and transfer tender squash to a blender.
  • To a blender, add butternut squash, sage, thyme, vegetable broth, salt and pepper. Puree until smooth and creamy. Set aside. Meanwhile, cook your pasta according to package directions, al dente. The pasta will continue to cook once you add it back to the puree, so cook to al dente to avoid overcooking.
  • To the same pot you used to simmer squash, melt butter or ghee. Add garlic, and cook, stirring frequently, until fragrant, about 2-3 minutes. Whisk in tapioca starch until lightly browned, about 1 minute. Gradually whisk in almond milk, butternut squash puree and Dijon mustard. Bring to a boil; reduce heat and simmer, stirring occasionally, until reduced and slightly thickened, about 3-4 minutes.
  • Add the cooked cooked elbow macaroni, grated cheddar, and Parmesan cheese. Stir until the pasta is evenly combined and the cheeses are melted. Top with additional Parmesan if desired.


  • To Store. Refrigerate leftover Butternut Squash Mac + Cheese in an airtight storage container for up to 4 days.
  • To Reheat. Warm leftovers on the stovetop in a saucepan over medium-low heat or in the microwave.
  • To Freeze. Freeze mac and cheese in an airtight freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before reheating.


Serving: 1g | Calories: 260kcal | Carbohydrates: 32g | Protein: 12g | Fat: 7g | Fiber: 4g
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