This butternut squash mac and cheese is a healthy makeover of classic macaroni and cheese nommed-up with whole-grain pasta, gruyere cheese, rosemary, and loads and loads of butternut squash! I’m telling you, it’s the most perfect comfort food casserole ever!!

Healthy Butternut Squash Mac and Cheese in casserole dish

I originally shared this recipe on October 19, 2012. I have updated the images and some of the text today. 

I have one word for you: HARVEST!!! I am drowning in produce, people. Send a lifeboat!

Okay, actually don’t send one, I am quite happy swimming in my produce pool. Hello there, Mr tomato…

Fact 1: I am addicted to buying all the locally grown produce when it is in season. I cannot help myself.

Fact 2: Right now on the counter, I am looking at 4 pounds (4 pounds!!!) of potatoes, a half pound of garlic, a bunch of kale, a dozen ears of corn and 24 squashes! Plus much, much more.

Observed Results of Fact 1 and Fact 2: I am trying to figure out a storage solution. I have my eye on some fancy schmancy-squash-curing-shelving-unit/alternative to a root cellar, but can you keep a secret? I actually want to start digging a real root cellar. It may happen. Just sayin’ I have the vegetables for it. So I am half-way there, right?

Or perhaps, my husband will build me a custom squash shelf… Jase, if you’re reading this… hint hint.

Healthy Butternut Squash Mac and Cheese with spoon

So with the bounty of the Vermont vegetable harvest, I am tucking vegetables into every single dish I make. This Macaroni and Cheese recipe for example, has an entire butternut squash in it. Boom!

There is both mashed butternut squash in the cheese sauce and chunks tossed with the noodles. Um, yum!!

Healthy Butternut Squash Mac and Cheese on a plate

So anywho, not that you need any further convincing about why your stove-top should be bubbling up with some cheesy sauciness, and then your oven should be wafting the savory notes of this comfot-food bakingness….

But if you do mayhap need extra convincing, then lemme say this… many of you over the years of my food blogging journey have told me that you like to serve mac and cheese at your Thanksgiving meals. First of all, I am so jealous about this tradition because I feel like I am missing out. I grew up in PA and we did not do mac and cheese at Thanksgiving. Second, a side note perhaps, as it is still harvest season and I am two moons away from actually making my Thanksgiving meal, but if you were to place a hot bubbling casserole of mac and cheese onto your Thanksgiving table THIS IS THE ONE!!!serving of Healthy Butternut Squash Mac and Cheese

Why This Butternut Squash Mac and Cheese is the Best!

  • A Whole Butternut Squash. You already heard about the entire butternut squash in it, so therefore it equates the essence of Pilgrims coming to your Thanksgiving table and giving you a most vanilla/platonic/reticent but still heart-felt high-five (okay it’s not that at all but um… what’s the word…. fallish). But dudes, this butternut squash mac and cheese is worthy of the Thanksgiving dinner table for more reasons.
  • Gruyere Cheese. It has Gruyere cheese in it. Therefore it is like grown-up mac and cheese. And the people you serve it to (even if they are your little people on a Tuesday night) will be like “Woah, how did you make this mac and cheese so special?”
  • Rosemary too. And there’s rosemary in it, so you’re like…like… almost… literally… Mario Batali all of a sudden. Yeah that’s it. In other words, it tastes great with the Gruyere and keeps the squash on the savory side.
  • Crunchy Topping. And the crunchy crispy breadcrumbiness. It is the deal sealer.

How did I do, did I convince you? Hope so! If it’s for a Tuesday or Friday in September or a special Thursday in November (Thanksgiving!!!!)… you gotta try this healthy mac and cheese recipe my friends. You won’t be disappointed. Please let me know if you do by coming back and leaving a comment below!

More Mac and Cheese Recipes To Try

This Macaroni and Cheese with Broccoli is a long time reader favorite. 

My Macaroni and Cheese with Cauliflower, Peas and Edamame is bursting with veggies, but that doesn’t stop kids from loving it!

This ultra creamy Gluten Free Mac and Cheese with prosciutto looks too good to be true! 

Stove Top Mac and cheese is always an easy weeknight option and so much better than boxed! 


Thanks so much for reading. If you make this Butternut Squash Macaroni and Cheese, please come back and leave a star rating and review! It is so helpful! 

Happy Cooking!


PS- Sign up for my email list to get recipes to your inbox every week.

Healthy Macaroni and Cheese with Butternut Squash- A fun fall twist of your favorite comfort food- the perfect addition to your Thanksgiving meal or for a kid-friendly weeknight meal | Healthy Seasonal Recipes @healthyseasonal #vegetarian

butternut squash mac and cheese

  • Author: Katie Webster
  • Prep Time: 45 minutes
  • Cook Time: 15 minutes
  • Total Time: 1 hour
  • Yield: 6 servings 1x
  • Category: Entree
  • Method: Baked
  • Cuisine: American


This butternut squash mac and cheese uses an entire squash and is the perfect addition to any fall meal. Sprinkle with breadcrumbs for a crunchy topping!



  • 4 cups cubed butternut squash, about 1 ¼ pounds
  • 2 cups whole-grain macaroni, 8 oz.
  • 1 tablespoon plus 1 teaspoon avocado oil or organic canola oil, divided
  • 2 shallots, chopped
  • 3 cups low-fat milk, divided
  • 1/3 cup all-purpose flour
  • 2 teaspoons Dijon Mustard
  • 1 teaspoon chopped fresh rosemary
  • ¾ teaspoon salt
  • ¼ teaspoon ground white pepper
  • 6 ounces shredded Gruyere cheese, about 2 cups
  • 3 tablespoons whole-wheat panko breadcrumbs, such as Ian’s
  • ½ teaspoon paprika


  1. Preheat oven to 400ºF. Coat a 2 quart baking dish with cooking spray.
  2. Meanwhile, bring several inches of water to a boil in a large saucepan fitted with a steamer attachment. Add squash and steam, covered, until very tender 8 to 12 minutes. Mash about half of the squash in a small bowl and set aside.
  3. Bring a large pot of water to a boil and cook macaroni 2 minutes less than package instructions. Drain and set aside.
  4. Heat 1 tablespoon oil in a large saucepan over medium-high heat. Add shallot, and cook, stirring often until softened and starting to brown, 1 to 3 minutes. Add 2 cups milk and bring to a simmer. Whisk the remaining 1 cup milk, flour, mustard, rosemary, salt and pepper in a small bowl until smooth. Whisk the flour mixture into the simmering milk, whisking constantly. Continue to cook just until the mixture bubbles and thickens. Remove from the heat.
  5. Whisk the Gruyere cheese into the thickened milk mixture until it is melted. Add the mashed squash and whisk until combined. Stir in the macaroni and the remaining squash. Transfer to the prepared casserole dish.
  6. Mix breadcrumbs with the remaining 1 teaspoon oil. Add the paprika and stir until evenly moist and bright orange. Sprinkle over the macaroni. Transfer to the oven and bake until bubbling hot and browned on top, 10 to 15 minutes. Let cool at least 10 minutes before serving.


  • Serving Size: 1 generous cup each
  • Calories: 401
  • Sugar: 10 g
  • Sodium: 459 mg
  • Fat: 15 g.
  • Saturated Fat: 6 g
  • Carbohydrates: 52 g
  • Fiber: 7 g
  • Protein: 19 g

More Comfort Food Recipes:

Healthy Roasted Garlic Mashed Potatoes

Cornbread Stuffing with Apples and Pecans

Pork Chops with Creamy Mushroom Gravy

Healthy Chicken Divan

Baked Meatball Parmesan

Here are some of the photos from the original post:

Butternut Squash with Rosemary