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.
Pin Print Review
3.86 from 57 votes
Prep Time15 mins
Cook Time30 mins
Total Time45 mins
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.

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Nutrition Facts
Butternut Squash Macaroni and Cheese
Amount Per Serving
Calories 432 Calories from Fat 135
% Daily Value*
Fat 15g23%
Saturated Fat 9g45%
Polyunsaturated Fat 1g
Monounsaturated Fat 3g
Cholesterol 43mg14%
Sodium 827mg34%
Potassium 274mg8%
Carbohydrates 55g18%
Fiber 3g12%
Sugar 7g8%
Protein 19g38%
Vitamin A 650IU13%
Vitamin C 5mg6%
Calcium 360mg36%
Iron 2.5mg14%
* Percent Daily Values are based on a 2000 calorie diet.

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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. 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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