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If you’re looking for a healthier twist on the classic comfort food mac and cheese, then look no further!

This healthy mac and cheese recipe is thick and creamy, with three types of cheese and comes together quickly on the stovetop!

Plus, your kids won’t even know they’re getting a serving of veggies in this clean eating meal.

Perfect for busy weeknights, try this delicious recipe today!

Healthy Weeknight Dinner That Your Kids Will Love

Please tell me I’m not the only mom with a picky eater!

My youngest, practically refuses to eat any vegetables, in fact I’m always looking for ways to sneak them into his meals.

Some nights he’s left sitting at the table to just try a bite or two of a vegetable.

It’s a real struggle in our home!

Well, I’ve found a way to sneak in a vegetable into his favorite dish, Mac and Cheese!

And the secret ingredient that makes this recipe so smooth and creamy is butternut squash.

Let me tell you, that Aiden has no clue this mac and cheese is loaded with healthy veggies.

Not to mention that the butternut squash gives it that same orange color of his favorite boxed mac and cheese.

To him, it’s just creamy, yummy goodness!

Healthy mac and cheese in a white serving bowl, garnished with Parmesan cheese.

Best of all, it can be made in less than 20 minutes, if you’ve already cooked the butternut squash.

To add the nutritional value of the healthy meal I also use whole wheat macaroni or pasta, along with light or reduced fat cheeses.

No one even realizes this thick and creamy sauce is good for them too.

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Is Boxed Mac and Cheese Unhealthy?

Mac and cheese is undeniably delicious, but if you’re looking to make it part of your regular pantry staples, think twice!

It has a high caloric content at 350 per one-cup serving along with high fat and sodium levels.

Healthy mac and cheese in a white serving bowl, garnished with Parmesan cheese.

What’s more – the real deal about boxed mac ‘n’ cheese?

Turns out that instead of using actual aged cheddar as we’re all led to believe, it contains mostly milk byproducts such as whey protein concentrate, plus artificial coloring agents or flavors are also thrown in there for good measure.

So prepare boxed mac and cheese occasionally, and make our healthy mac and cheese recipe a regular at your home.

How Long Will It Keep?

Just made a delicious batch of mac and cheese? Awesome!

To keep it just as flavorful for days after, store in an airtight container in the refrigerator.

Looking to preserve your leftovers even longer?

Pop them into individual portions in freezer-safe containers – they’ll stay tasty up to two months, for when you’re ready for seconds (or thirds!).

When it’s time to warm up again, microwave at 75% power and stir every minute or so until piping hot.

Enjoying homemade goodness never tasted this easy!

Jump to Recipe

Healthy Mac and Cheese Ingredients

Ingredients for mac and cheese, whole wheat pasta, mashed butternut squash, cheddar cheese, Parmesan cheese, Swiss laughing cow cheese wedges, sour cream, milk, garlic, salt and pepper.

For this recipe you’ll need macaroni or pasta, I prefer whole wheat.

You’ll also need a medium to large butternut squash, laughing cow creamy swiss cheese wedges, reduced fat cheddar cheese, grated parmesan cheese, garlic, milk, sour cream, salt and pepper to taste.

Pretty simple and basic ingredients, but combined together, its pure bliss!

Prepare Butternut Squash

My favorite way to prepare the butternut squash is with my slow cooker.

I learned this tip from my mom.

When they were remodeling their home and were without a kitchen for about 6 weeks she started experimenting with her slow cooker.

She found the best way to cook squash and baked potatoes when you don’t have an oven was in the slow cooker.

You simply wash, half and seed the squash.

Wrap each squash half in aluminum foil and place in a slow cooker.

No need to add any moisture, with the squash wrapped in foil.

Set the temperature to high and it will be ready in about 4 hours, or on low 7-8 hours.

This works great with baked potatoes too!

Have you tried cooking squash or baked potatoes like this?

When the butternut squash is cooked and soft, scoop into a large pan or dutch oven.

Prepare Pasta

Add whole wheat elbow macaroni to salted boiling water and cook on the stovetop until tender.

First salt the pasta water and bring to a rapid boil.

Salted water makes all the difference in the flavor of the pasta, so go ahead and salt it!

If you’re concerned about the sodium levels in the recipe if you salt the water, did you know that cooking 1 pound of pasta in 1 gallon of water containing 1 tablespoon of table salt adds about 55 mg of sodium per ounce of pasta.

Which would be the equivalent to 1/2 tsp. of salt per serving.

To make gluten-free mac and cheese, just use gluten-free rice or bean pasta.

Prepare Creamy Cheese Sauce

Add chicken broth to the mashed butternut squash and heat in a heavy pan on the stovetop.

To make this delicious and creamy butternut squash cheese sauce, place the mashed squash in a large pan.

Place the pan over medium heat and add the chicken broth.

Add garlic, salt and pepper to the mashed butternut squash in a large pan, heat until garlic is cooked.

As it starts to heat, add in the garlic, salt and pepper to taste.

Cook for 1-2 minutes until the garlic begins to cook.

Whisk in until melted 3 laughing cow cheese wedges into the butternut squash mixture in a pan.

Open the wedges of laughing cow cheese and whisk into the butternut squash mixture.

Stir until the cheese is incorporated into the squash.

Add cheddar cheese and Parmesan cheese to the pureed butternut squash in a heavy pan on the stovetop.

At this time, add the cheddar and parmesan cheese, whisk until smooth and creamy.

Add sour cream and milk to the butternut squash mixture in a heavy pan on the stovetop.

Finally add the sour cream and milk and whisk until smooth.

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Combine Macaroni and Cheese Mixture

Stir healthy mac and cheese sauce with a whisk until smooth on the stovetop.

You now have the most flavorful, creamy cheese sauce for your healthy mac and cheese.

Add cooked whole wheat pasta to the butternut squash and cheese sauce on the stovetop.

Once the pasta is tender, drain and add to the cheesy butternut squash mixture and stir until combined.

Stir cooked pasta into to the healthy mac and cheese sauce on the stovetop.
Stir in cooked whole wheat pasta in the the butternut squash, mac and cheese sauce.

Garnish with additional parmesan cheese and serve hot.

Healthy mac and cheese in a white serving bowl, garnished with Parmesan cheese.

This healthy mac and cheese recipe is perfect for busy weeknights!

It’s creamy, with three types of cheese, and has veggies in it – all while being kid-approved.

Plus, it comes together quickly on the stovetop making it ideal for busy nights.

What are you waiting for?

Try this comforting recipe today and enjoy a delicious meal the whole family will love.

More Healthy Comfort Foods

Healthy mac and cheese in a white serving bowl, garnished with Parmesan cheese.

Creamy Mac and Cheese with Butternut Squash

This thick and creamy mac and cheese has three types of cheese and butternut squash. It comes together quickly on the stovetop making it perfect for busy weeknights! Plus, your kids will never know they're getting a serving of vegetables in this clean eating recipe that’s kid-approved! Try this comfort recipe today!
Prep Time 5 minutes
Cook Time 10 minutes
Total Time 15 minutes
Course Main Course, Side Dish
Cuisine American
Servings 8 serving


  • large pan, dutch oven
  • whisk


  • 3 c. whole wheat pasta, dry
  • 1 butternut squash, cooked, mashed – Butternut squash from your grocer's freezer may be substituted.
  • 1/2 c. chicken broth
  • 1 tsp. garlic, minced
  • 5 wedges light laughing cow, creamy swiss
  • 3 oz. reduced fat cheddar cheese
  • 2 T. freshly grated parmesan cheese
  • 1/2 c. milk – 2%, 1%, or skim
  • 2 T. sour cream
  • salt and pepper to taste


Cook Pasta

  • Bring 4 quarts of salted water to a rapid boil. Add pasta and cook 9-10 minutes until tender. Drain.

Prepare Cheese Sauce

  • Prepare cheese sauce while cooking the pasta.
    Place cooked and mashed butternut squash into a deep pan, like a dutch oven over medium heat.
    Add chicken broth, garlic, salt and pepper to taste. Heat for 1-2 minutes until garlic is cooked.
    Add laughing cow cheese wedges and whisk into the butternut squash mixture.
    Add cheddar and Parmesan cheese, stir until cheese is melted.
    Add sour cream and milk and stir until incorporated.
    Keep warm.

Combine pasta with cheese mixture.

  • Once the pasta is cooked and drained, add to the butternut squash cheese mixture.
    Heat through and serve.
    Optional, garnish with additional Parmesan cheese.


My favorite way to cook butternut squash is wrapped in foil and placed in my slow cooker. It takes about 4 hours on high, or 8 hours on low. This can be done in the morning you plan to make this meal or the day ahead.
The butternut squash can be baked in the oven at 350° for 1 1/2 hours. Cover it in foil to keep it moist.
In a pinch you can use fresh or frozen, diced butternut squash and steam it in the microwave.
Keyword cheesy, comfort food, creamy, dinner under 30 minutes, healthy, healthy mac and cheese, kid-approved, kid-friendly, quick and easy

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Pinterest image, healthy homemade mac and cheese garnished with additional parmesan cheese.

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