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Healthy Mac And Cheese | Make It Healthy

This healthy mac and cheese recipe uses butternut squash, unrefined flour, greek yogurt, and all clean eating ingredients to make the best healthy mac and cheese ever!

Categories Clean, gluten free, Healthy, Kid-Friendly, Vegetarian
Difficulty Easy
Keyword healthy mac and cheese, healthy mac and cheese recipe, low calorie mac and cheese
Prep Time 25 minutes
Cook Time 25 minutes
Total Time 50 minutes
Servings 8
Calories 287 kcal
Author Lacey Baier of A Sweet Pea Chef


  • 16 oz quinoa noodles (2 boxes)
  • 3 cups butternut squash (approx. 1/2 squash), cubed
  • 1/2 yellow onion, diced
  • 2 cloves garlic, minced
  • 1 1/2 cups plain almond milk
  • 1 1/2 cups low sodium chicken broth
  • 1/2 cup plain greek yogurt
  • 1 1/2 tsp sea salt, divided
  • 3/4 tsp black pepper, divided
  • 1 tbsp chickpea flour
  • 1/4 cup parmesan, grated
  • 1/4 cup almond meal
  • 1/4 tsp garlic powder


  1. Preheat oven to 350 degrees.
  2. Fill a deep pot with water and bring to a boil. Once boiling, add the quinoa noodles and cook until almost tender, about 6-7 minutes.

  3. While the noodles are cooking, add the cubed butternut squash, onion, garlic, almond milk, and chicken stock to another pot and cook over medium-high heat. Allow to simmer until the butternut squash is tender.

  4. In a small bowl, combine the parmesan cheese, almond meal, remaining 1/2 tsp. sea salt, remaining 1/4 tsp. pepper, and garlic powder and mix well. Set aside.

  5. Once tender, carefully transfer the butternut squash contents to a blender and puree until very smooth. This process may require you to blend in batches.

  6. Add 1/2 tsp. sea salt, 1/2 tsp. ground black pepper, the greek yogurt, and the chickpea flour and blend again. Taste for seasoning and add any additional salt or pepper as needed.
  7. Drain the cooked noodles and return to the pot.
  8. Pour the butternut squash mixture over the noodles and stir to incorporate.
  9. Pour the macaroni and cheese mixture into a casserole dish.

  10. Sprinkle the parmesan mixture evenly over the top of the mac and cheese.
  11. Place into the oven and bake for 20-25 minutes, or until the top is golden brown.

Recipe Video

Nutrition Facts
Healthy Mac And Cheese | Make It Healthy
Amount Per Serving (1 cup)
Calories 287 Calories from Fat 36
% Daily Value*
Fat 4g6%
Saturated Fat 1g5%
Cholesterol 3mg1%
Sodium 568mg24%
Potassium 258mg7%
Carbohydrates 55g18%
Fiber 2g8%
Sugar 2g2%
Protein 9g18%
Vitamin A 5605IU112%
Vitamin C 12mg15%
Calcium 144mg14%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.