Featured comment
So delicious! The butternut squash puree made it so creamy in combination with the cheese. This is my new go-to mac and cheese recipe!
Watch How To Make This Recipe
No, I Really 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.
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.
- White Cheddar Mac and Cheese with Squash and Toasted Walnuts.
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. No messing around with texture. Just smooth delicious sauce, creamy melted cheese, and noodles to bring it all together.
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 happy.


Ingredients In This Recipe
Not to worry, there’s still cheese in this mac and cheese, but there are also a lot of delicious and nutritious things too! Here’s what you need:
- Macaroni
- Butter
- Onion
- Butternut squash
- Broth
- Milk
- Cheese
If you’re looking for ingredient substitutions, jump down to the FAQ!

How To Make Healthy Mac and Cheese
This mac and cheese is so easy, and my favorite part is that the sauce just gets whizzed up in a blender. Essentially, there are only three steps to getting this from “I want some mac and cheese” to getting it on the table.
- Cook the Macaroni: Boil on the stove in water, as usual.
- Make the Sauce: Sauté the onion, cook the squash in broth, and blend it together with the milk.
- Combine: Mix together the blended sauce and noodles, and add the cheese. Stir and EAT!
Perfect in every way. I love this so much.

Frequently Asked Questions About This Recipe
Yep! Just use a dairy-free milk, and skip the cheese. It’ll be a saucier sauce, but still delicious. Alternatively, you can try this amazing vegan mac and cheese!
Yep! And if you like garlic instead, you could use sautéed garlic in place of onion.
Yes (kind of). I would stick to winter squashes that are similar to butternut so you get the right texture – acorn, honeynut, buttercup, and kabocha should all work in place of it.
Yes! This works great served alongside a meat main dish (like this air fryer chicken) or I could see some chicken meatballs being delicious as well.
In the mac and cheese itself, green peas are always a good option! You can add them to the boiling noodles for the last few minutes of cooking. Otherwise, a side of broccoli would be so good too.
Yep! Just use your favorite gluten-free noodle.
Healthy Mac and Cheese
- Total Time: 50 minutes
- Yield: 4 – 1 heaping cup per serving 1x
Description
Healthy Mac and Cheese: one heaping cup of comfort food for just under 400 calories. Simple, creamy, homemade goodness. So good!
Ingredients
- 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
Instructions
- Cook Macaroni: Cook the macaroni according to package directions. Drain and set aside.
- Sauté Onions: 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.
- Cook Squash: 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.
- Blend Sauce: Add the onions, milk, salt, and reserved broth and puree until completely smooth and creamy. This should yield about 4 cups sauce.
- Mix Together: 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.
Notes
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
- Method: Stovetop
- Cuisine: American
Nutrition Facts
- Daily value: 10% Total Fat 7.9g
- Daily value: 6% Cholesterol 19.1mg
- Daily value: 61% Sodium 1399.1mg
- Daily value: 25% Total Carbohydrate 69.8g
- Daily value: 33% Dietary Fiber 9.3g
- Sugars 10.6g
- Daily value: 30% Protein 14.8g
- Daily value: 90% Vitamin A 811.5µg
- Daily value: 34% Vitamin C 30.7mg
- Daily value: 17% Iron 3.1mg
- Daily value: 18% Potassium 829.8mg
- Daily value: 28% Phosphorus 346.9mg
Keywords: healthy macaroni and cheese, healthy mac and cheese, mac and cheese, veggie mac and cheese






I have made this recipe pretty much every month for years. Tonight I decided to tweak it slightly (for curiosities sake more than anything else). I added a block of Japanese curry blocks (s&b golden curry), i heated three of the five into the milk before adding the milk into the blender I added the other 2 at the end after tasting. To add to the katsu curry feel I added the pasta into a baking dish and topped with Panko breadcrumbs.
Worked really well (helped having a great base recipe to start with)
But will picky kids know the squash is in there? The 10 year old in my family is EXTREMELY picky and sniffs out veggies like a bloodhound! Then the gig is up and she won’t TOUCH it.
Hello, it looks great, if I can trick my kids in eating a vegetables why not. Just wondering what is the sodium in this recipe?
“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”
Yikes with this sentence! Every body fits in a swimsuit. Let’s get rid of “healthy” in a recipe title.
I want to try these recipes. I need to expand my variety of recipes that I make.
Very well written; love the use of the squash, that’s an inspired idea!
I just made this and it is delicious! Next time I’ll add 2/3 of the sauce to the noodles to check that there’s a good sauce to pasta ratio. This batch came out a little more saucy than my preference but that’s ok🙂
Tastes great!
Love it! Mac and cheese that i dont feel guilty about. Wondering if this works as well with almond or any milk alternatives
I was following this until you made a fat phobic comment about fitting into a swimsuit. Maybe you can do some reflecting around that as it’s 2021 and we are so sick of bodies being shamed.
Oh my goodness. I’m in my first trimester of pregnancy after losing three babies, and this time around I’ve just been kind of giving into cravings/the only things I can stomach (which are only carbs and cheese…), figuring I need something to stress about less. However, I finally decided I needed to figure out how to get some veggies in me. THIS!
I did add a few carrots & cauliflower to the butternut to get a bit more varied nutrients & cut a bit of butternut sweetness. But, MAN! This pasta is a nutrient miracle for this nauseous pregnancy-after-loss mom. Thank you!
So glad you enjoyed it, Brynna! All the best to you ❤️
This was delicious!!! Thank you for sharing. So nice to have a healthier alternative for a classic comfort food.
A co-worker made this with a participant at work yesterday. She gave me a bowl and I was blown away! My daughter is a vegetarian, but doesn’t always eat healthy (fries are vegetarian…sigh). I love to cook, she loves to eat. I am so making a double batch. One for her, one for me! Due to Covid we don’t visit indoors so I just drop off things I think she’ll like. She will love this, and I’ll feel good about giving her a daily portion of the ever important orange vegetables 🙂
Has anyone saved the excess broth to drink or reuse?
The proportions of this dish are all wrong. I made a half recipe and the pasta was swimming in squash. It was just a pureed mess.
If you have not made this, it is a must! I boiled my butternut squash in homemade chicken broth and used whole milk and a little heavy cream (I know that makes it more calories). The squash sauce was creamy and flavorful. I also added sautéed chicken and steamed broccoli to the mac & cheese for a more complete meal. I doubled the amount of squash and broth, so I also added more cheese than called for. But my ratio worked out well. I used white sharp cheddar. It was so good. My husband really liked it too and it was the perfect comfort food for a cold December night!
I have little ones who I desperately am trying to expose to all kinds of healthy foods. The first time I made this the kids couldn’t get past the texture of the onions. My sister, however, was absolutely delighted by the leftovers and it was the first thing she asked me to bring over! I used only a quarter of an onion the second time and it was a winner all around. My kids absolutely devoured it! This is so much healthier than boxed options and really doesn’t take that much longer to make!
So happy your family loves the recipe, Krystal!
Used zucchini instead of squash – my family loves it!!
YUM!
Tried this tonight for the first time. It was so easy and delicious! I used Kraft Sharp Cheddar Melts (shredded cheese with cream cheese mixed in) because that’s what I had on hand. I also added a crunchy panko topping. My 9 year old son/self-proclaimed mac-and-cheese connoisseur loved it! Went in for 2nds and 3rds, even after I told him what the “secret ingredients” were. Thank you!
Love hearing this, Christa! Thanks for sharing. 😊
This is delicious roasted the squash used whipping cream and a mixture of cheddar & guyere
YUM YUM YUM!
Sooooo good. I made this tonight because I was craving Mac n cheese but wanted it with a healthy spin. The only thing I’ll say is it was a little to onion-y for me so next time I will use less onion. Otherwise so yummy and easy!!
Glad you enjoyed this, Selma!
=)
Love the butternut squash in the sauce! Genius. Can’t wait to try this out. Thanks so much for sharing, Lindsay!
Enjoy!
I am AMAZED at this recipe!! There is nothing I would do differently if I were to do it again. Flavor is spot on, and it fills you up without the heavy feeling you sometimes get with regular Mac n cheese, well done!!!
So happy to hear you enjoyed this, Megan! 🎉
So excited to make this! Do you think sweet potatoes can be used in place of butternut squash? Trying not to go to the store this week.
We haven’t tried that substitution yet, but it’s worth a shot. Let us know how this goes!
LOVE this recipe! Have made it a handful of times. If I’m using canned butternut squash for a shortcut, how much canned should I use? Thanks!
We’d suggest about 2 15-ounce cans. 🙂