Butternut Squash Mac and Cheese

This butternut squash mac and cheese is deliciously smoky from the smoked Gouda cheese, and has a few handfuls of spinach for added nutrients.

Smoky Mac and Cheese with Squash and Spinach

Here’s another one to add to our series of “things I used to eat out of a box”. We’ve tackled mashed potatoes, pizza, brownies, hot chocolate, croutons, and salad dressing, all with the goal of making “real food” out of something that’s readily available in highly processed form. So what’s next? Our dear friend Katelyn put forth a challenge a few weeks ago – mac and cheese. And what a perfect contender for the real food challenge!  I grew up on the processed “cheese food” version of the stuff, and then in college graduated to the powder-packet cheese version.

How to Cut Butternut Squash

Making butternut squash mac and cheese

I’ll admit, those packages are comforting – and we cast no judgment on anyone who is a fan!  But we thought it would be interesting to create a version that was full of nutrients AND include the delicious taste of pasta and cheese – using ingredients from our local market. And it turned out to be one of our favorite butternut squash recipes to date!

A quick search of “healthy” mac and cheese recipes shows butternut squash puree is starting to show up as a substitute for some of the richness in the creamy cheese sauce. This got my mind turning on squash – but why go to the labor of a puree? We left the squash in cubes, threw in some spinach from the market, and used smoked gouda to add a delicious smoky flavor, with a bit of Greek yogurt to round it out (in place of butter).

If you count calories, you might not see a huge difference with this version versus its counterpart. What you do get is a delicious homemade meal rich in nutrients – with the same comfort quotient of a traditional mac and cheese. And the verdict from our taste testers? Katelyn’s words were: “best recipe ever”…but you’ll have to try for yourself!

Related: Stovetop White Cheddar Mac and Cheese


Video: How to cut butternut squash

The most challenging part of this butternut squash mac and cheese is cutting the butternut squash! To show you how we do it, here’s a video of me cutting butternut squash in our kitchen.

Looking for more real food recipes?

Outside of this butternut squash mac and cheese, here are a few typically “box” or “bottle” recipes re-made with all whole food ingredients:

This butternut squash mac and cheese is…

Vegetarian. For gluten-free, use gluten-free noodles.

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Butternut Squash Mac and Cheese

1 Star2 Stars3 Stars4 Stars5 Stars (5 votes, average: 5.00 out of 5)

  • Author: a Couple Cooks
  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Total Time: 30 minutes
  • Yield: 4 1x


This butternut squash mac and cheese is deliciously smoky from the smoked Gouda cheese, and has a few handfuls of spinach for added nutrients.



  • 1 medium butternut squash (3 cups chopped)
  • 1 bunch spinach or baby spinach leaves (3 cups chopped)
  • 3 garlic cloves
  • 1 medium shallot (1/4 cup minced)
  • 12 ounces whole wheat penne
  • 1 1/2 tablespoons olive oil
  • 1 1/4 teaspoon kosher salt, divided
  • 2 cups smoked Gouda cheese, shredded
  • 1 cup cheddar cheese, shredded
  • 1/4 cup Greek yogurt
  • 1/2 to 1 cup milk


  1. Dice the butternut squash following the video instructions. Roughly chop the spinach (or omit for baby spinach). Mince the garlic. Mince the shallot.
  2. Start a large pot of salted water to boil. When boiling, add the pasta and cook until tender.
  3. Meanwhile, in a large skillet, heat the olive oil. Place the squash cubes in the skillet with 1/4 teaspoon kosher salt and sauté until soft and a bit browned, about 10 minutes, stirring occasionally. If the pan gets too dry, add a bit of water to let the squash steam. Once the squash is tender, add the spinach and cook until wilted, about 2 minutes. When the spinach is wilted, turn off the heat. Add the minced garlic and shallot, and cover the skillet until the pasta is done.
  4. When the pasta is done, drain it. Immediately, combine the following in a large bowl: pasta, squash and spinach mixture, shredded smoked Gouda cheese, shredded cheddar cheese, Greek yogurt, and 1 teaspoon kosher salt. Stir to combine. Add more milk (or cheese or yogurt) as necessary to get a creamier texture. Serve immediately.
  • Category: Main Dish
  • Method: Stovetop
  • Cuisine: American

Keywords: Butternut squash mac and cheese, Mac and Cheese, Comfort Food, Vegetarian Dinner Recipes, Butternut Squash Recipes

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About the Authors

Sonja Overhiser

Cookbook Author and writer

Sonja Overhiser is author of Pretty Simple Cooking, named one of the best healthy cookbooks of 2018. She’s host of the food podcast Small Bites and founder of the food blog A Couple Cooks. Featured from the TODAY Show to Bon Appetit, Sonja seeks to inspire adventurous eating to make the world a better place one bite at a time.

Alex Overhiser

Cookbook Author and photographer

Alex Overhiser is an acclaimed food photographer and author based in Indianapolis. He’s host of the food podcast Small Bites and founder of the recipe website A Couple Cooks. Featured from the TODAY Show to Bon Appetit, Alex is author of Pretty Simple Cooking, named one of the best vegetarian cookbooks by Epicurious.


  • Reply
    January 23, 2012 at 2:13 am

    I love the smoky flavor idea! Can’t wait to try this with acorn squash. Yum!

  • Reply
    Lauren @ Healthy Food For Living
    January 23, 2012 at 7:12 am

    I’m a huge fan of incorporating squash into cheese sauces, and I bet the smoked Gouda is fantastic in this mac & cheese!

  • Reply
    Katrina @ Warm Vanilla Sugar
    January 23, 2012 at 7:27 am

    This sounds lovely! I need a new mac&cheese in my life!

  • Reply
    January 23, 2012 at 11:03 am

    Oh gosh so many magical words here. Mac and cheese, smokiness, squash, garlic, spinach. Need. This. In. My. Belly. So curious about the yogurt addition too. Thanks for sharing!

  • Reply
    Tiffany {A Clove of Garlic}
    January 23, 2012 at 11:17 am

    Sounds amazing! I love that this mac&cheese is not heavily loaded with cheese — yet still sounds like it will hit the spot. All great tasting ingredients, so I am sure it will be wonderful!

  • Reply
    January 23, 2012 at 11:27 am

    This needs to get in my belly as soon as possible. Yum!

  • Reply
    Heidi @ Food Doodles
    January 23, 2012 at 12:00 pm

    I was literally just thinking about how nice it would be to have something with smoked cheese in it. That makes this look especially good to me right now :D I love the color the squash gives it – beautiful! I’m really curious about the yogurt addition, that must make it nice and creamy.

  • Reply
    Alicia @ The Humble Foodie
    January 23, 2012 at 1:08 pm

    Yum, I love the idea of adding squash and spinach to mac and cheese. I always used to combine the boxed version with some frozen peas for a cheesy “mac and peas” dish, but fresh vegetables sound a lot more flavorful!

  • Reply
    Sylvie (A Pot of Tea)
    January 23, 2012 at 2:37 pm

    This looks and sounds delicious. I like that you add in vegetables for a more balanced meal without giving up on the comfort of mac n’ cheese.

  • Reply
    Fran {The Flavorful Fork}
    January 23, 2012 at 4:03 pm

    I am a huge fan of butternut squash! Just had some yummy butternut squash risotto for lunch today. I need to try this recipe out for sure. I especially like the addition of the smoky gouda cheese. Thanks for the inspiration!

  • Reply
    January 23, 2012 at 9:35 pm

    I can attest that squash and gouda make the best mac n cheese… I’m not surprised your friend loved it so much!

  • Reply
    Christi's Chirps
    January 24, 2012 at 10:26 am

    This recipe sounds amazing! I love the addition of squash. A warm, cheesy dish is the absolute best on a cold winter day. Tomorrow’s forecast is chilly with torrential rain. Sounds like the perfect day for some smoky mac and cheese. :)

    Thanks for sharing. Happy Tuesday.


  • Reply
    Krissy {Krissy's Creations}
    January 24, 2012 at 11:00 pm

    Mac and Cheese is my favorite! I love a recipe that is both healthy and delicious, and this recipe hits the mark perfectly. Yummmm

  • Reply
    January 29, 2012 at 9:21 pm

    I tried a recipe very similar to this recently and I just can’t get excited about squash in my mac & cheese. Sorry. The gouda is a great choice to pair with it but I would rather see the gouda shine more instead of having to share the spotlight with the squash.

  • Reply
    February 8, 2012 at 10:05 am

    Your blog is making me SOOOOOOOO hungry. Which is a problem, because it’s 8am and I need to eat breakfast food. Not mac and cheese. But oh my goodness, I cannot wait until I feel well enough to go to the grocery to pick up a squash.

  • Reply
    February 10, 2012 at 9:29 pm

    Hi guys, I just made this and it’s very tasty! I undercooked my butternut squash, but even so, I really enjoyed it. Somehow, despite not having a true sauce, it turns out to be quite creamy and rich. Thanks much!

    P.S. Thanks for adding the veg amounts in cups–so helpful with something like squash that varies so widely in size.

    • Reply
      February 11, 2012 at 10:30 pm

      So glad you liked it! You’ll have to try it with buttercup squash too if you ever find any — it’s very tasty as well!

  • Reply
    March 16, 2012 at 10:43 pm

    Just finished making this and had to share–IT’S DELICIOUS! Perfect consistency, great flavor, and so easy to make. Thank you for sharing! I’ll definitely be storing this in my recipe collection.

  • Reply
    June 28, 2012 at 3:11 pm

    If I WANTED to puree the squash (extras for the baby), how much would you say I should use?

    • Reply
      June 28, 2012 at 3:37 pm

      Good question! I would guess around 2 cups pureed or so. Let us know how it turns out!

  • Reply
    Christina Dooley
    November 7, 2012 at 7:06 pm

    Love this! I think I undercooked the butternut squash a bit (I got a little impatient with the 2-yr. old distracting me). Also, Tim made me add a bit of shredded chicken, since he’s not a huge fan of vegetarian dishes, but I stuck to the recipe with everything else, and we loved the smokey flavor of the Gouda & the tangy flavor of the Greek yogurt. Even our 6 yr. old enjoyed the change. Thanks. Can’t wait to make it for friends:)

    • Reply
      November 11, 2012 at 4:40 pm

      Oh, so glad you enjoyed it, friend! Thanks for trying it out :)

  • Reply
    September 8, 2014 at 6:56 pm

    This recipe was so good. I tried it today but, instead of spinach, I used beet leaves (I bought fresh beets the day before at farmers market and they came with all the yumy leaves) and instead of low fat milk, I used almond milk and for cheese, I used fresh shredded parmesan cheese. Turned out really yuummy!

  • Reply
    December 13, 2014 at 8:13 pm

    I was looking for a mac n cheese recipe on the entirety of the internets and then honed my search back into my sweet spot here. That stuff was amazing. I really like the shallots that give it a little crunch in there. Also used acorn squash instead of butternut – you can’t buy a “medium sized” butternut squash. The store only carries Starbucks-like sizes of Tall, Grande, and Venti (aka Large, Large, and 20). In any case that’s a killer recipe – will definitely be featured on the menu of the couple cooks restaurant.

    • Reply
      December 14, 2014 at 12:19 pm

      Haha,you crack me up! SO glad you enjoyed this one! How is the A Couple Cooks restaurant coming about? :)

  • Reply
    October 25, 2016 at 4:23 pm

    WOW! This was AMAZING. My husband bought a butternut squash with no plans and I nearly jumped out of my chair when I saw this pop up on my news feed.

    I used Squid Ink pasta and it made a great Halloween dinner! I also used the (non smoked) cheese I had on hand, so I added smoked salt, smoked paprika, and sriracha.

    Seriously an amazing and hearty dish!

    • Reply
      October 25, 2016 at 8:12 pm

      Ooo so glad you loved this! Makes me want to make it again, we haven’t in ages. Thanks so much for letting us know!

    • Reply
      October 25, 2016 at 8:34 pm

      PS and meant to say LOVE the Halloween themed pasta with squid ink! How inventive :)

  • Reply
    January 26, 2019 at 1:57 pm

    This was delicious!Thank you for a new, nutritious Mac & cheese recipe to add to my repertoire :)

    • Reply
      January 27, 2019 at 1:53 pm

      You’re so welcome. Thanks for making it!

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