Butternut Squash Mac & Cheese is sooo delicious you won’t believe it.  This recipe “sneaks” in squash and nobody will notice because all of the creamy goodness.  Just feast your eyes on this photo, it sure looks mouth-watering. This  Mac and Cheese recipe gets its creaminess from the Greek yogurt and cheese.  The pinch of nutmeg adds a delightful touch of savory to the dish.

Butternut squash is rich in anti-oxidants in the article from the Academy of Nutrition and Dietetics article in May 2020. Anti-oxidants protect healthy cells which helps prevent cancer, heart disease and cataracts.

If you like squash recipes, you may also like to try these popular recipes:

As you know, we like to eat with our eyes.   Did you know that our dietitian Kaitlin Williams Eckstein, MPH, RD, LD created this recipe, cooked and photographed it too!  This recipe can be adapted to be gluten-free by using gluten-free pasta as indicated in the recipe below.

Butternut Squash Mac & Cheese

Feel like you have to give up mac & cheese if you want to eat healthy? Want to see how long I can yell "NEVAHHHHH"?
Course: Main Dish, Side Dish
Cuisine: American, Gluten Free, Vegetarian
Keyword: Easy, Fall, Fiber, High protein, Holiday, Kid-friendly, Meal prep, Party, Winter
Cooking Method: Oven, Stove Top
Condition: Cancer, Gluten Free, Heart Health, Low Sodium, Nut Free, Vegetarian
Servings: 6 servings


  • 1 medium butternut squash peeled and chopped
  • 1/2 onion chopped
  • 2 cloves garlic minced
  • 1 tbsp olive oil
  • 2 tbsp thyme fresh, chopped
  • 1 lb pasta whole wheat or gluten-free; cooked and drained
  • 3/4 cup vegetable broth low sodium chicken or vegetable
  • 1/2 cup milk
  • 1/2 cup Greek yogurt nonfat plain
  • Pinch of nutmeg
  • salt and pepper to taste
  • 8 oz cheese shredded cheese of choice
  • 1/4 cup parmesan cheese finely grated
  • cooking spray


  • Preheat oven to 400ºF.
  • Toss butternut squash, onion, and garlic in olive oil. Sprinkle with 1 Tbsp thyme. Lightly sprinkle with salt and pepper. Roast in the oven for 30-40 minutes, until soft and browned. Once removed from the oven, reduce heat to 350ºF.
  • In the meantime, cook pasta according to package directions.
  • When the butternut squash is done, place in a blender with your broth of choice, milk, yogurt, and nutmeg, and blend until smooth.
  • In a large bowl, combine pasta with squash puree. Mix in your cheese of choice (reserving 1/4 cup for topping), and 2 Tbsp fresh, chopped thyme, if desired. Salt and pepper to taste.
  • Spray casserole dish lightly with cooking spray. Spoon noodle mixture into the dish and lightly sprinkle with remaining cheese and parmesan cheese.
  • Cover with aluminum foil and bake for 20 minutes. Uncover and continue to bake for 20-30 minutes, until bubbling and lightly browned.


Carbohydrates: 75g | Protein: 25g | Fat: 18g | Sodium: 444mg | Potassium: 724mg | Fiber: 5g

If you like our Butternut Squash Mac Cheese, please let us know in the comments below.

Please note:

Nutrition info is an estimate and may contain errors.

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An award winning recipe developer, Dietitian Kaitlin’s mission is to empower others to reach their health goals by encouraging them to get back into the kitchen. Co-author of Nourished: 10 Ingredients to Happy, Healthy Eating and Cooking with Diabetes.