Healthy Mac and Cheese Recipe - Skillful Cook
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Healthy Mac and Cheese

101 reviews / 4.6 average

No, really. I mean it. Healthy Mac and Cheese.

Like mac and cheese that is healthy. Noodles with sauce that will secretly give you vegetables. Creamy sauce without boatloads of butter and flour. Favorite comfort food that packs a little nutrition.

Backing up, though. It's getting to that time of year when WINTER IS TOO COLD. I say that with a massive amount of guilt as I recall the many times that I begged the weather gods to send a polar vortex to the Philippines last year. But we'll leave that in the past. This is the now, and right now, I'm done being cold.

Also please add this to the list of things I'm done with: having a cold. The bad news is it will not be done with me. Like, come on already justgetoutofhere. And to make matters all the more winter-dramatic, as I was writing this I just used the last Kleenex in the house and sent Bjork a panicked text to please pick up some Kleenex right now. SOS ASAP OMG haaaalp.

When I have a cold//when it is cold outside//when both happen at the same time//all year round any time no matter what, I like to ease my soul with foods like healthy macaroni and cheese.

How To Make Our Healthy Mac and Cheese (1 MIN):

Healthy Mac and Cheese: one heaping cup of comfort food for just 350 calories. Simple, creamy, homemade goodness. So good! |

I've been making variations of this recipe for the last few years, but always with extra stuff in it, because, you know, the whole food blog thing.

For example, Butternut Squash Mac and Cheese with Caramelized Onions, Apples, and Bacon.

Or White Cheddar Mac and Cheese with Squash and Toasted Walnuts.

At the moment, I'm getting sort of annoyed of my toasted-walnuts-in mac-and-cheese ways, so I'm giving it to you straight up, in all it's plain creamy wonderfulness: Healthy Mac and Cheese. No need to fancify. Especially if you're sick. Which, if you are, please just come over and we'll eat this and watch the Cesar Milan being the amazing Dog Whisperer and feel glad that just have colds and not red zone dogs. Truth: Netflix and a cold and me left alone for too long can bring out some weird times.

This healthy mac and cheese is perfect for times when you don't want anything really far outside of the box. Like, literally, nothing too far from the powdered cheese noodle dinner that comes in a blue box. Just maybe a little healthier and homemade. And more vegetables and less butter. Bonus.

If that's you (and if you can't tell, it's definitely me right now), then this is your stuff.

Healthy Mac and Cheese: one heaping cup of comfort food for just 350 calories. Simple, creamy, homemade goodness. So good! |

One of my favorite things about this saucy + healthy mac and cheese is the inclusion of a caramelized onion in the pureed sauce. The flavor gets a warm depth to it without the issue of the caramelized onion pieces floating around in there. Heeey now, don't look at me like that. Because normally I love things like pieces of caramelized onion and maybe when this cold leaves me alone I'll be back to that sort of bold, dangerous eating. But this is the day when we're sticking to plain-Jane. No messing around with texture. Just smooth delicious sauce, creamy melted cheese, and noodles to bring it all together.

Healthy Mac and Cheese: one heaping cup of comfort food for just 350 calories. Simple, creamy, homemade goodness. So good! |

So if I were to have a bottom line here, it would be this -> make the sauce, cook some noodles, shred some cheese, and be a happy mac and cheese eating person who still fits into a swimsuit. Because summer is coming. I can feel the sun on my face right now. Ready? Here it comes. One two three now. Three two one summer. Ready set go. Sun. Come. Bam. Snap. Poof.

Just... I'll work on that.

Healthy Mac and Cheese: one heaping cup of comfort food for just 350 calories. Simple, creamy, homemade goodness. So good! |

Other Mac and Cheese Goodness

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A picture of Healthy Mac and Cheese

Healthy Mac and Cheese

  • Author: Skillful Cook
  • Total Time: 50 minutes
  • Yield: 4 - 1 heaping cup per serving 1x


Healthy Mac and Cheese: one heaping cup of comfort food for just under 400 calories. Simple, creamy, homemade goodness. So good!


  • 2 cups uncooked elbow macaroni - whole wheat, low glycemic, gluten free... any will work!
  • 1 tablespoon butter
  • 1 small yellow onion
  • 1 small butternut squash (4-5 cups cubed)
  • 5 cups chicken or vegetable broth
  • 3/4 cup milk
  • 1 teaspoon salt
  • 2/3 cup shredded cheese - I like Gruyère but any kind will work
  • parsley for topping
  • salt and pepper to taste


  1. Cook the macaroni according to package directions. Drain and set aside. Heat the butter in a large skillet over medium low heat. Cut the onion into thin rings and add to the butter in the pan, sauteing over low heat until fragrant and golden, about 20 minutes.
  2. Meanwhile, remove the skin and the seeds from the squash. Cut the flesh into small cubes. Bring the broth to a boil and add the squash. Cook for 5-7 minutes or until fork tender. Drain, reserving 1/2 cup broth, and transfer squash to the blender. Add the onions, milk, salt, and reserved broth and puree until completely smooth and creamy. This should yield about 4 cups sauce.
  3. Pour the pureed sauce over the cooked noodles and add the shredded cheese. Stir to melt the cheese; add water or milk to adjust consistency as needed. Serve with parsley, salt, and pepper to taste.


When caramelizing the onions, keep the heat low to prevent burning. The deeper the golden color, the more flavorful they will be.

  • Prep Time: 10 mins
  • Cook Time: 40 mins
  • Category: Dinner
  • Cuisine: American

Keywords: healthy macaroni and cheese, healthy mac and cheese, mac and cheese, veggie mac and cheese

Healthy Mac and Cheese - A classic dish made with butternut squash for a healthy twist! Full of cheese and flavor |

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  1. Skillful Cook Logo

    I love the fact that healthy and mac and cheese are in the same sentence! So brilliant to add caramelized onions right into the pureed sauce! I still haven’t tried the whole squash in sauce thang…but this means it’s gotta happen!

  2. Skillful Cook Logo

    I put butter nut in sauces for the natural colour booster and for its sweet taste with out the addition of sugar; this is my fave trick for adding creamy textures to coconut cream free curries too. Fully rooting for this mac and cheese to be at my kitchen table.

    1. Skillful Cook Logo

      What a great idea – I would have never thought of that! I’m going through an almond butter phase so I’ll have to try it out!

    2. Skillful Cook Logo

      What is butter nut? How much do you add and does it replace something?! Thank you!

  3. Skillful Cook Logo

    Send Out Sissues!!!!!!
    Be well. I’m coughing very healthily 😉
    No no no. No healthy mac and cheese. Mo nothing except pasta and cheese please. I bought…..looks around to see if anybody’s around..whispers..1lb of cheese..ssshhh…….
    Any case I’ve never caramelised anything and I don’t want onions in my mac and cheese which I’ve only made once in my life.

  4. Skillful Cook Logo

    Oh my gosh Lindsay! Love this! I am so excited that the sauce is made with squash and it look amazing. Where did you find your cute white bowls?

    And so sorry about your cold, hope you get feeling better soon. I’m ready for winter to be done too 🙂

  5. Skillful Cook Logo

    What a great idea, the sauce looks smooth and creamy, this should lift your spirits, hope your cold gets better quickly. Have Bjork pick up the LOTION infused kleenex. Your nose will thank you.

    1. Skillful Cook Logo

      OH MY GOSH so funny you would say that – he bought these extremely posh aloe-infused Kleenex for me and they are like silk on my face. I love them so much.

  6. Skillful Cook Logo

    I love this healthy mac and cheese – I have a butternut version posted, but it doesn’t have the carmelized onion. Genius! Must add. When my kids were younger, I used to sneak in carrots and they seemed to like it better than plain old mac and cheese! Gotta love it.

    Polar vortex in the! Here in the Philly region the snow is bad too. I’ve had enough!

  7. Skillful Cook Logo

    Can you believe I’ve never actually made a proper mac and cheese? Or proper cookies, or a proper layer cake … I have to fix these things! Love the look of this version of m & c with its hidden veggies all pureed into it. Very tempted to give it a try! ‘Perastika!’ as they say here in Greece (get well soon!)

    1. Skillful Cook Logo

      How funny – I just made a layer cake this weekend too for Bjork’s birthday! I was hoping to post the recipe but… it’s … demolished. 🙂

  8. Skillful Cook Logo

    You must have read my mind! I just bought a butternut squash and was trying to figure out what to do with it! Thanks so much.

  9. Skillful Cook Logo

    This is the 3rd post in a row I’ve read where the blogger is sick! Hope it’s not contagious through the inter-webs 🙂 Regardless, I’m going to be making this soon! Delicious, and such a wonderful and healthy idea!

  10. Skillful Cook Logo

    This looks divine! Unfortunately I had to remove all dairy from my diet this year but I will be surprising my hubby with this treat for sure. Great pictures as well (although they are always great on this site), makes me want to dive right in.

  11. Skillful Cook Logo

    Okay, clearly you knew I was craving mac and cheese but also feeling guilty about said craving and refusing to give in. 😛

    Thanks so much for sharing this! I may need to use acorn squash (there are three slooooowly ripening in my pantry), but this will definitely appear on my table this week!

  12. Skillful Cook Logo

    Feel better soon!!!

    This looks soooo yummy – and totally kid friendly! Love that the caramelized onion is in the sauce. My littlest one will truly pick out every single little tiny speck of onion. Why? I don’t know. I think it’s delicious! 🙂 But now … now my kids will never know! Mwahahahaha!

  13. Skillful Cook Logo

    I’ve never really been much of a fan of Mac and Cheese, but this actually appeals to me a million times more. I love butternut squash.
    My favourite pasta dish I’ve been making for yonks is actually Macaroni Peas! Where I whizz Peas up in the food processor. It’s . amazing. I’m looking forward to trying yours (minus the butter and cheese. . it’s the whole vegan thing!)

  14. Skillful Cook Logo

    GIRL. I’m in the unpleasant first trimester of pregnancy and food has been tricky. I just made this and OH MAN. Pregnancy gold mine. I don’t want to let myself go, but the only things that seem apetizing to me right now are carbs. I made this recipe with qunioa noodles and hid a heaping serving of sauteed spinach in the bottom of the bowl and it was delicious. Healthy comfort food. Boom.

    1. Skillful Cook Logo

      Aw, that makes me so happy. I was actually thinking of all you sicky preg moms out there.. my sister is pregnant and during her first tri she could only stomach cheese and carbs. 🙂 glad you enjoyed it Katy! And congrats!