Healthy Butternut Squash Mac and Cheese

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Mac and cheese is a kids favorite everywhere. It’s quite easy to make if you use the prepared kits from the grocery store, but it’s not healthy. I’d much rather serve my children this healthy butternut squash mac and cheese I came up with after tasting my friend’s version.

Healthy butternut squash mac and cheese

One fall day I arrived at my friends house to find her and her kids eating baked macaroni and cheese, so when she invited my son and I to join them for some, we couldn’t resist. I mean… who doesn’t love macaroni and cheese, right?!? And hers was delicious! 

When our kids were done eating and ran off to play she whispered, “Don’t tell them but it’s actually a healthy macaroni and cheese with butternut squash recipe!”

I had never heard of before, but she explained that she had cooked it with butternut squash, and her kids were getting their vegetables and didn’t even know it. I asked for the recipe, but forgot and left her house without it. But thanks to the Internet, I came up with my own version and it came out as good or better after a few tweaks.

Healthy Mac and Cheese With Butternut Squash

In this mac ‘n cheese recipe, not only is squash a secret ingredient, but I also added Gruyere cheese, one of the best baking cheeses around.

Gruyere cheese is also great for melting, used in fondue, and to melt on top of French onion soup.  It is slightly salty and has an earthy flavor that pairs well with the squash, and a perfect addition to standard macaroni and cheese recipes.

In this recipe I used prepackaged butternut squash to save time, and you can easily find it these days. When we don’t have a fresh garden harvest of butternut squash we buy ours from Costco or Wholefood, and you can often even find it organic.

If you have a garden and fresh butternut squash on hand you can substitute for the equivalent amount fresh, which is about 10 ounces or four cups. Just peel your squash, cut it in half lengthwise, take out the seeds, and chop up the rest into cubes.

My family has been eating this mac ‘n cheese for a few years now and has never known that every time they were getting seconds and thirds, they were also getting a lot of vitamin A, vitamin C, potassium, and even protein from the hidden squash inside.

I’m always looking for comfort food, that my family can eat without the guilt of empty calories. This recipe becomes even more healthy by using whole grain pastas such as quinoa pasta, which has a higher protein content than wheat pasta and is also gluten free.

I hope your family loves this mac and cheese with butternut squash just as much as mine does. We’d love to hear if you make it and see your photos.

Variation – Butternut Squash Mac ’n’ Cheese Muffin Cups

Spoon the mac into muffin tins lined with lightly greased cupcake papers (or, better yet, use these reusable silicone baking cups)and sprinkle with panko topping if desired.

Bake at 400°F for 15 minutes. Easy to eat – no utensils required 😋

This healthy baked butternut squash mac and cheese is a must try for every family: easy to make, creamy, cheesy, tasty, and yet healthy. Your kids will ask for seconds and thirds, and you'll be glad to know they are getting their vitamins ;) #Butternut #Squash #MacAndCheese #HealthyFoodRecipes #Baked #Recipe #Tasty #Creamy #Simple #Pasta #HowToCook #SideDishes #Dinner #Vegetarian #Microwave #Lunch #Snack #Breakfast #LowCarb #InstantPot #TasteOfHome #Keto #InOven #HowToMake

Contributions From the Community

More Ideas to Make This Butternut Squash Mac and Cheese Even Better

I made this tonight and it was good. Normally I use a variety of cheeses, next time I’ll do that. I also add spinach and a can of Ro-tel to my Mac and cheese.

It needed a few more seasonings, but overall, I’ll def make it again, especially if my neighbor continues planting a plethora of butternut squash.
~Jean Janeri

Great ideas! Thanks, Jean!

Healthy Butternut Squash Mac And Cheese

This healthy butternut squash mac and cheese with Gruyere cheese is AMAZING and a great way to sneak in some extra vegetables for picky palates.
Don't let the 16 steps concern you. They're each broken down into simple and logical progression to make it easy to follow and do.
Prep Time 30 minutes
Cook Time 30 minutes
Total Time 30 minutes
Course Casseroles & Loaves
Servings 12
Calories 354 kcal


  • Olive oil to coat dish
  • 3 cups shredded cheddar cheese
  • 1/2 cup panko bread crumbs
  • 1/2 cup grated Parmesan cheese
  • 1/2 tsp dried thyme or 1 tsp fresh
  • 4 Tbsp butter (½ stick)
  • 1/4 cup all-purpose flour
  • 2 cups whole milk
  • 1/2 cup vegetable broth we like the Pacific Organic Mushroom or Vegetable broths
  • 1 tsp dry mustard
  • 1/2 tsp paprika
  • 1/2 tsp garlic powder
  • 10 dashes hot sauce optional
  • 1 egg beaten
  • 1 cup shredded Gruyère cheese
  • 1, 10- ounce package frozen butternut squash thawed, (or 3-4 cups fresh cubed and cooked)
  • 1 tsp. salt
  • 1/2 tsp. Freshly ground black pepper optional
  • 1 lb. pasta spiral, elbow, or similar (cooked al denté and drained well)


  • PREPARE SQUASH: Defrost if using frozen; Cook if using fresh, then mash using a potato masher. Set aside.
  • COOK PASTA according to package directions, but a couple minutes less to keep it al denté.
  • PREHEAT the oven to 400°F. Lightly coat a 9 x 13-inch baking dish with olive oil.
  • COMBINE 1 cup of the cheddar, panko, parmesan, and thyme in a small bowl; set aside for topping.
  • MELT butter in a large saucepan over medium-low heat to make the sauce. Sprinkle in the flour and whisk constantly for about 5 minutes until smooth and creamy.
  • POUR in milk in a slow, steady stream, followed by the broth, whisking constantly over medium-low heat.
  • ADD herbs and seasonings: mustard, paprika, garlic powder and hot sauce (if using).
  • COOK ~5 minutes or so, whisking constantly, until thickened.
  • CRACK the egg into a separate small mixing bowl and slowly whisk in about 1/4 cup of the warm sauce to temper the egg (else the heat could cook it), then add the egg mixture to the rest of the sauce and whisk.
  • ADD remaining 2 cups cheddar and the Gruyère cheese and whisk to melt as it forms a thick cheese sauce.
  • REMOVE from heat and stir in the mashed butternut squash until smooth.
  • SEASON to taste with salt, pepper and hot sauce (if using).
  • STIR in the pasta and gently toss to coat well.
  • POUR into the prepared dish.
  • TOP with the reserved cheddar-panko mixture sprinkled evenly over the pasta.
  • BAKE about 20 minutes until golden and bubbly.


Serving: 1gCalories: 354kcalCarbohydrates: 23gProtein: 16gFat: 22gSaturated Fat: 12gPolyunsaturated Fat: 8gCholesterol: 74mgSodium: 652mgFiber: 2gSugar: 3g
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