Butternut Squash Macaroni and Cheese

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Butternut squash macaroni and cheese, classic comfort food with a healthy twist! Whole grain noodles combined with creamy cheese sauce and crunchy panko.

Butternut squash macaroni and cheese

I have to admit, this luscious bowl of macaroni and cheese has a secret… it’s made with butternut squash! A traditional macaroni and cheese recipe has flour, butter, milk, and cheese base to make the sauce. Given to opportunity to incorporate a vegetable packed with nutrients in each bite and still get a creamy texture, I went for it!

When thinking about making healthier meals, I like to use techniques that help to build flavor. The start of this dish begins with slowly caramelizing onions in a little bit of butter. Caramelizing the onions over medium to medium-low heat creates a sweet and savory flavor, adding a lot more depth to the macaroni dish.

Healthy version of macaroni and cheese

As your onions are happily transforming in the pan, it’s time to make the sauce! Boiled until fork-tender, cubes of butternut squash are the base for your creamy sauce. The natural starch in the squash is activated when heated, so when pureed the rapid mechanical shear from the blades, in addition to the milk and both help to create a super silky base.

I’ve found that my blender is a pro at making purees, and I love the sound of it humming while it goes to work on those veggies! Don’t forget to add those caramelized onions to the sauce for blending, it’s going to take it to the next level.

The beauty of this dish is that you can add whatever cheese to it you like. I usually use a blend of Monterey Jack and cheddar in my classic macaroni and cheese, but I stuck to a simple sharp cheddar with the butternut squash.

Butternut squash macaroni and cheese in a white bowl with panko breadcrumbs

Since the squash provides the creaminess, I just needed to choose a piece of cheese that added flavor, and good aged cheese is a fantastic choice. Other options could be parmesan, gruyere, smoked gouda, or combining a few, just go for it!

If you have always had the more traditional macaroni and cheese recipe, I’m not going to say that it’s like having a 1:1 replacement. You can tell there is more texture, a tiny more grainy because you are using a vegetable for the sauce compared to just a milk and cheese base. However for a healthy alternative, this is an excellent option, and I’m pretty choosy when it comes to mac n’ cheese.

A spoonful of golden noodles combined with butternut squash

I’ve been choosing whole grain, whole wheat or fiber-enriched pasta for my family meals. Pasta technology has been pretty phenomenal as consumers are becoming more health-conscious yet still want to enjoy their favorite dishes with added benefits.

I’m trying to incorporate nutrients wherever I can, and I’m glad that there are so many varieties to choose from nowadays. For a little crunch, I toasted some wheat Panko bread crumbs and sprinkled them on top of each bowl, ah the icing on the cake.

How does the butternut squash make such a creamy cheese sauce?

Butternut squash is considered a naturally starchy gourd. When it’s cooked then pureed, the starch molecules absorb the liquid from the milk and broth. Then it swells and holds the moisture in suspension very nicely and doesn’t separate. What you get is creamy, thickened and smooth sauce without having to make a roux base (cooked flour and butter plus milk). Not only is butternut squash an awesome ingredient, but it’s also got some nice health benefits too! It’s low in fat, packed with dietary fiber, potassium, vitamin B6, folate, vitamin C and the very obvious carotenoids in the orange flesh like beta-carotene that converts to vitamin A. (Source: www.wholeliving.com)

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Butternut Squash Macaroni and Cheese

Butternut squash macaroni and cheese, a classic comfort food with a healthy twist! Whole grain noodles combined with creamy cheese sauce and crunchy panko.
4.57 from 60 votes
Prep Time15 minutes
Cook Time30 minutes
Total Time45 minutes
Servings 4 servings
Course Entree
Cuisine American


  • 2 cups elbow macaroni
  • 1 tablespoon unsalted butter
  • 1 ½ cups yellow onion, thinly sliced, ⅛-inch
  • 4 cups butternut squash, cubed, ½-inch
  • 5 cups chicken broth, or vegetable broth
  • ¾ cup reduced-fat milk, 2%
  • 1 teaspoon kosher salt, more to taste
  • 1 cup sharp cheddar, shredded
  • black pepper
  • ¼ cup breadcrumbs, panko
  • parsley, chopped for garnish


  • Heat butter in a large skillet over medium heat. Add the onions in one layer in the pan. Reduce heat to medium-low and cook until tender and lightly golden, about 25 to 30 minutes, occasionally stirring, keeping the onions in one layer. You want the onions caramelized not crisp and brown. Reduce heat if the onions brown too quickly or start to burn.
  • While the onions cook, bring the broth to a boil in a large pot. Add the butternut squash and cook for 7 minutes, or until tender. Drain the squash, reserving the broth, transfer squash to the blender.
  • Add cooked onions, milk, 1 teaspoon salt, and ¼ cup reserved broth. Add up to ¼ cup more broth if desired to thin the sauce. Puree until very smooth and creamy.
  • In a medium-sized pot, cook macaroni in salted boiling water according to the manufacturer's instructions. Drain and set aside.
  • Pour the sauce over the cooked noodles and add the shredded cheese. Stir to melt the cheese, add more milk if needed to adjust the consistency. Season with salt and pepper to taste.
  • In a small nonstick pan, toast panko breadcrumbs over medium heat until all sides are toasted, keeping them moving in the pan, about 3 minutes.
  • Added toasted breadcrumbs and parsley to garnish the macaroni and cheese.

Nutrition Facts

Serves: 4 servings
Calories 432kcal (22%)Carbohydrates 55g (18%)Protein 19g (38%)Fat 15g (23%)Saturated Fat 9g (45%)Polyunsaturated Fat 1gMonounsaturated Fat 3gCholesterol 43mg (14%)Sodium 827mg (34%)Potassium 274mg (8%)Fiber 3g (12%)Sugar 7g (8%)Vitamin A 650IU (13%)Vitamin C 5mg (6%)Calcium 360mg (36%)Iron 2.5mg (14%)

Percent Daily Values are based on a 2000-calorie diet. All nutritional information is based on estimated third-party calculations. Each recipe and nutritional value will vary depending on the brands you use, measuring methods, and portion sizes per household.

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Jessica Gavin

I'm a culinary school graduate, cookbook author, and a mom who loves croissants! My passion is creating recipes and sharing the science behind cooking to help you gain confidence in the kitchen.

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24 Comments Leave a comment or review

  1. Ann@CreatedToCook says

    Jessica… You are such an awesome mom! I still make this for my boys (11 and 6), and because they’ve never had the stuff from the box, they don’t know the difference. Keep up the great work!

    • Jessica Gavin says

      Thank you Ann! I get super happy when James like my cooking, especially when it’s a healthier version! We need to reconnect! How’d the blog going?

    • Jessica Gavin says

      Thank you Raquel! Mac n cheese always seems like an indulgent treat, but happy to have this healthier version as an option!

    • Jessica Gavin says

      Hi Nicole! I have a FREE ebook if you sign up for my newsletter on the right side of my website, 25 recipes! I hope to create more cookbooks to share in the future 🙂 Your comment really made me smile!

  2. Stacey says

    This sounds amazing! I love butternut squash and I love mac & cheese so I’m looking forward to trying the two together. I like to get extra veggies into meals where I can so this really appeals. ?

    • Jessica Gavin says

      Thank you Stacey! I really enjoy the combo. I love how my toddler can enjoy the recipe and get extra veggies too!

  3. Maxine says

    Having grown up with the boxed stuff, I was afraid that my teenage boys would not like like it. I was wrong!! They loved it, and the winner for me is that it’s so much healthier, packed with vitamins. This one’s a keeper! The leftover broth has now been enhanced and will make a great base for a soup. Thanks Jessica!

    • Jessica Gavin says

      Thank you for the wonderful feedback Maxine! I grew up on the boxed too, and I definitely enjoy this recipe and so does baby James 🙂 Great use of the extra broth for a soup!

  4. Jill says

    This was just okay. I love caramelized onions and butternut squash but I felt like the onions were lost in this dish. It was a lot of work and mess and I would have rather had a plate with caramelized onions, butternut squash baked in the oven, and a protein like steak. This didn’t satisfy my Mac n cheese craving. It was more like butternut squash noodles, and I would have rather saved the carbs and had a protein. Overall, not bad- I’ll eat the leftovers, but I won’t be making it again.

    • Jessica Gavin says

      Hi Jill! I truly appreciate your honest feedback on the butternut squash macaroni and cheese. It’s definitely a different spin on a classic. I would love to help improve the recipe anyway I can 🙂

  5. Jo says

    This was fantastic! My husband loved it, which is a great plus. I was in a hurry to find a side dish for a pork loin roast and discovered the pin for this on Pinterest. As I was short on time, I made several modifications but can’t wait to try the exact recipe. I did not use onions and instead added some garlic and instead of squash I used a can of pumpkin purée. Thanks

  6. Morgan says

    This is awesome! Definitely going to try with Banza pasta- so much more protein and better tasting than whole grain 🙂

  7. Sam says

    I have made this three times now! Absolutely love this recipe and it is really easy to modify. (One time I put in almond milk, another time I put in some indian spices for flavor) This is also a really good recipe if you have some leftover veggies in your fridge (like yams or similar) and you don’t know what to do with them! Love love love this recipe. Thanks!!

    • Jessica Gavin says

      Thank you so much for your feedback Sam! I love how you’ve kicked it up a notch 🙂 I’ll have to give your modifications a try!

  8. Jan says

    Would there be a way to make this in the Instant pot? Somehow cook the broth, squash and noodles all together after sauteing the onions?
    Has anyone tried?

    • Jessica Gavin says

      Hi Jan- I wonder if you can make the sauce portion in the pot and pressure cook the vegetable, puree, and then cook the noodles on the saute setting until tender, then mix in the cheese.

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