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Butternut Squash Mac and Cheese

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Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!

Butternut Squash Mac and Cheese
Butternut Squash Mac and Cheese

A few weeks ago I posted this Cauliflower “Mac” and Cheese recipe that swapped out pasta for cauliflower. Today I bring you this guilt-free mac and cheese recipe. Giving you all the comfort of the classic dish, but with an extra heaping of nutrients.

Butternut Squash Mac and Cheese

Hey there, I’m Heather K. Jones—I’m a dietitian, the nutrition expert for the Skinnytaste cookbooks, and the founder of the weight and wellness program, Feel Better Eat Better. If you struggle with emotional eating or weight anxiety, be sure to check out my free Masterclass by clicking RIGHT HERE. You’ll find out the exact steps I teach my clients to create lasting success from the inside-out, even if they’ve tried everything.

This guilt-free mac and cheese gives you all the comfort of the classic dish, but with an extra heaping of nutrients. Made with whole-wheat noodles, three cheeses (Gruyere, cheddar and Parmesan), shallots, and lots of good-for-your-body butternut squash… it’s cozy, creamy AND nourishing! This is a new staple for me and my sisters. Just add a big green salad and you have the perfect anytime meal.

butternut in the blenderwhite sauce with butternutwhite sauce with butternut squashButternut Squash Mac and CheeseButternut Squash Mac and Cheese

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Butternut Squash Mac & Cheese

4.73 from 84 votes
Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!
Course: Brunch, Lunch, Side Dish
Cuisine: American
Butternut Squash Mac and Cheese
Prep: 15 mins
Cook: 1 hr
Total: 1 hr 15 mins
Yield: 8 servings
Serving Size: 1 cup


  • Olive oil spray
  • Kosher salt
  • 1 pound cubed butternut squash
  • 10 ounces whole wheat elbow pasta
  • 1 ½ cups low sodium vegetable broth divided
  • ½ teaspoon onion powder
  • ½ teaspoon garlic powder
  • ¼ cup panko breadcrumbs
  • 2 tablespoons freshly grated Parmesan cheese
  • 1 tablespoon unsalted butter
  • 1 medium shallot minced
  • ¼ cup all-purpose flour
  • 2 cups skim milk
  • ½ cup shredded gruyere cheese
  • ½ cup shredded cheddar cheese
  • Chopped chives optional, for garnish


  • Preheat oven to 375 degrees F. Spray a 9” x 11” glass baking dish with oil and set aside.
  • Bring a large pot of salted water to boil. Add squash and boil until tender, 5-6 minutes.
  • When fork tender, transfer squash with a slotted spoon to a blender.
  • Add pasta to boiling water and cook according to package directions. When cooked, drain and put back into the pot.
  • Meanwhile, add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon salt and black pepper, to taste to the blender with the squash. Blend until smooth and creamy.
  • In a small bowl, combine breadcrumbs, Parmesan, ¼ teaspoon salt and pepper. Set aside.
  • Melt the butter in a medium sauce pot over medium heat. Add the shallots and sauté 2 minutes. Sprinkle the flour evenly over the shallots and cook another minute.
  • Add the remaining 1 cup broth and milk and whisk to combine. Bring sauce to a boil, then reduce heat to medium-low and cook 5 minutes, whisking frequently.
  • Remove pot from heat and whisk in cheese, pureed squash, 1 1/2 teaspoons salt and pepper.
  • Add sauce to noodles, gently mix to combine, then transfer mixture to prepared baking dish.
  • Sprinkle with breadcrumb mixture and bake 25 minutes. Switch oven to high broil and broil for 2-3 minutes, or until crumbs are starting to brown.

Last Step:

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Serving: 1 cup, Calories: 275 kcal, Carbohydrates: 43 g, Protein: 13 g, Fat: 7 g, Saturated Fat: 4 g, Cholesterol: 21 mg, Sodium: 462 mg, Fiber: 4.5 g, Sugar: 5 g


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169 comments on “Butternut Squash Mac and Cheese”

  1. Huge hit with my whole family. My husband was shocked when I told him it had butternut squash in the sauce! I oven baked it in a 9×13 pan, and added an three ounces of squash, and three ounces of noodles, so my proportion was slightly different from the recipe. I will be in our rotation

  2. Love this recipe! Have already made it 3 times within the past 2 months. People always ask for me to share the recipe

  3. Darn… really wanted to like this recipe, but it wasn’t salty or flavorful? I added 2x more cheese and a bit more salt, but it seemed like something ended up drowning out the mac’s taste 🙁 I just didn’t want to add even more sodium though,. I guess I need to tinker this to my liking.

    1. 1.5 teaspoons of salt are added in this recipe, in step 5 & 9. Cheese is salty, so when making a cheese substitute from butternut, adding enough salt is important to get that cheese-like flavor. I might try white miso next time.

      1. you could also try adding a tsp of Dijon mustard to the sauce to kick up the cheesiness. 

    2. I completely agree. I was really disappointed. All of that work and all those ingredients and it tasted like nothing. I’m followed the recipe to the T. Strange! 

  4. This dish is tasty and a fun combination of two fall staples. I paired it with a simple side salad to get some more veggies in (and also so that I wouldn’t be tempted to eat my weight in pasta).
    I tried to follow the recipe in general, but I did roast my butternut squash for added flavor and because I just couldn’t bring myself to boil them; it felt wrong. I also ended up using rigatoni instead of elbows just to make it look pretty. I used more cheese than called for because personally when I’m making mac’n’cheese, the healthiness of the dish isn’t my primary concern.
    Ultimately, my family and I enjoyed it and I would make it again. But it did feel like a labor of love and it turned my kitchen upside down. So, for me it is more of a special treat of a recipe than a weekday staple. Would recommend it though!

  5. Wow was this good! I made this with regular macaroni (to appease the husband) and subbed in chicken stock for veggie broth, plus oat milk instead of skim. We didn’t feel like we were eating ‘healthy’ Mac n cheese at all. It was very savory, and comfort food-y, nothing seemed lacking! I never would have guessed that I could have had such a delicious Mac n cheese with so little cheese/other heavy stuff.

  6. This is my favorite guilt free mac and cheese recipe. Flavor is great. Agree that pre-bake it does look VERY runny but as long as you whisk according to the recipe and then bake the liquid evaporates to a normal consistency. I generally add broccoli to the sauce before I bake for extra veggies and 1/2 tsp paprika to the breadcrumb mixture for some extra flavor! 

  7. I thought this recipe was good, but definitely could’ve been better! I agree that there is quite a bit of sauce and it kind of took away from the cheesiness. In the video it looks way gooey-er. I might use more cheese and maybe a half cup less stock next time then just adjust the calories. My kids ate it so that was a plus 🤷🏼‍♀️ 

  8. Looks delicious, looking for meals for my toddler. Does this freeze well? Would love to make a big batch.

  9. Loved this recipe so much!! To anyone who is concerned that the pasta is “drowning” in the sauce- don’t worry! I also thought that, but it all worked out during the baking part. It came out perfect and not at all soupy. Just an FYI because I see a lot of comments with people adding extra pasta and you really don’t need to! 

  10. Avatar photo
    Kim L Wilczyk

    Hi. This recipe looks very delicious. I was wondering if you can use frozen butternut squash in this recipe.


    1. Avatar photo
      Kristin Keating

      I used frozen and it came out fine! I have those frozen cube pouches from Costco and just cooked them in the microwave and then tossed in the blender. Definitely made the recipe so easy!

  11. Do you think I could trick my hubby into believing this is just mac&cheese or would he catch on to the butternut squash? He is picky about “different” vegetables even if he hasn’t actually tried squash before…. he will refuse to try it if he figures it out ahead of time!  (I did not rate the recipe because I haven’t made it – yet!)

    1. My dad is extremely picky and only eats my mom’s mac and cheese (which she makes with Velveeta). The first time I made this I sent some home with my mom and my dad ate it not knowing it had butternut squash in it. He said it’s a very close second to my mom’s. I also made mine with Havarti cheese instead of gruyere. This is my new go-to mac and cheese recipe…so good and freezes well too!

  12. This was a great mac and cheese recipe. Loved the extra nutrients the squash provides while still providing that creamy, cheesy taste. I didn’t have a 9″x11″ pan (seemed like I had everything but that size) and used a 9″x13″ with success. Will definitely serve to my grandchildren the next time we can share a meal together. I’m sure they will gobble it up.