5 from 8 votes
Overhead photo of Healthy Mac and Cheese garnished with sliced scallions in a white saucepan with ramekins of sliced scallions and grated cheese next to the pan.
Healthy Mac and Cheese
Prep Time
20 mins
Cook Time
30 mins
Total Time
50 mins

Macaroni and cheese gets a skinny makeover with a creamy butternut squash infused cheesy sauce!  This healthy mac and cheese is thick and creamy, easy to prepare and the perfect way to satisfy all your cheesy cravings without all the guilt!!

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Course: entree, Main Course, Side Dish
Cuisine: American
Keyword: cheese, Healthy, macaroni, skinny
Servings: 8
Calories: 325 kcal
  • 1 Pound Elbow Macaroni (or small dry pasta of choice)
  • 2 TBS Unsalted Butter
  • 1 small Yellow Onion - grated (about heaping 1/2 cup)
  • 1 Pound Butternut Squash - peeled and 1/2-inch dice (about 3 1/2 to 4 cups)
  • 1/2 scant tsp EACH: Ground Nutmeg, Dried Thyme & Smoked Paprika
  • 1 ½ Cups Half-and-Half
  • 1/2 Cup Low-Sodium Vegetable or Chicken Stock
  • Kosher Salt and Ground Black Pepper , to taste
  • 1 ½ heaping Cups Grated Sharp White Cheddar Cheese (about 3 ½-4 oz.) (SEE NOTES)
  • 1/3 heaping Cup Finely Grated Parmesan Cheese - plus more for serving
Optional for Serving: Fresh Thyme, Scallions or Parsley
  1.  Boil water for pasta:  Bring a large pot of water to a boil. 

  2. Sauté onions and squash:  While water is coming to a boil, heat the butter in a separate large pot over medium heat.  Add the onion and cook for 2-3 minutes, stirring occasionally.  Add in the squash and season with nutmeg, thyme, paprika, 1 teaspoon salt and ½ teaspoon pepper.  Cook, stirring, for 2 minute. 

  3. Add liquid and simmer:  Add in the half-and-half and stock.  Increase heat to medium-high and bring to a simmer.  Immediately reduce heat to maintain a gentle simmer.  Cover and cook until the squash is extremely tender, about 20-22 minutes.  Turn off heat.

  4. Meanwhile, cook pasta:  Generously season boiling water with salt.  Add the pasta and cook to al dente according to package directions.  Drain the pasta, reserving ½ cup of the pasta water, and set aside.

  5. Puree sauce:  Once the squash is tender, use an immersion blender to puree the squash and stock mixture until smooth and creamy.  Alternatively, transfer the squash mixture to a stand blender in batches and puree until smooth.  Return the squash puree to the pot.

  6. Add seasoning and cheese:  Turn heat to low and add both cheeses gradually, 1 handful at a time, whisking until smooth between each addition.  Taste the sauce and adjust for seasoning with salt and pepper.

  7. Add pasta:  Add the cooked pasta to the sauce and stir until the pasta is coated and combined with the sauce.  Add some of the pasta water if the sauce is too thick.

  8. Serve:  Ladle the mac and cheese into individual serving bowls and garnish with fresh herbs and more parmesan if desired.  Enjoy!

Recipe Notes
  1. To save time on prep, purchase already peeled and cubed butternut squash from the grocery store. (It can be found in the produce section of most major grocers.)
  2. Make sure you purchase a good quality, sharp cheddar cheese for this recipe.  And, shred the cheddar yourself!  Pre-shredded cheese has a white coating and additives that prevent the cheese from smoothly melting.  I used a sharp aged cheddar.  
  3. Use the small holes on a box grater to finely shred the cheese.
  4. The butternut squash cheese sauce can be prepared a day in advance and stored in an airtight container in the refrigerator.

 Nutritional information is an approximation and based upon 8 servings.

Nutrition Facts
Healthy Mac and Cheese
Amount Per Serving
Calories 325 Calories from Fat 81
% Daily Value*
Fat 9g14%
Saturated Fat 5g31%
Cholesterol 25mg8%
Sodium 86mg4%
Potassium 398mg11%
Carbohydrates 52g17%
Fiber 3g13%
Sugar 3g3%
Protein 9g18%
Vitamin A 6306IU126%
Vitamin C 13mg16%
Calcium 90mg9%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.