Butternut Squash Mac and Cheese with Caramelized Onions, Bacon, and Apple

Butternut Squash Mac n' Cheese with Caramelized Onions, Bacon, and ApplePinitI have a thing for butternut squash mac n’ cheese, mostly because I have a thing for secretly healthy things that don’t seem healthy.

But the butternut squash is just the beginning.  In case you didn’t notice by the longest blog title ever, there is a ton of good stuff in this mac and cheese, because sometimes I just need to add in everything.

And by everything, I mean caramelized onions, fresh crispy sweet apples, and crispy bacon.

Are you in love yet?  My stomach is happy and so are my skinny jeans and so is my husband.  This is a delicious miracle!

Now, for the moment of truth.

Nutrition Facts for Butternut Squash Mac n' Cheese

Come on, you can uncover your eyes.

This mac n’ cheese is almost guilt-free!

And I guess if you wanted to be a little weird, you could leave out the cheese for an even more guilt free (but still creamy and super delicious) meal!

Butternut Squash Mac n' Cheese

4.7 from 23 reviews
Butternut Squash Mac n' Cheese with Bacon, Caramelized Onions, and Apples
Prep time: 
Cook time: 
Total time: 
Serves: 4
  • ½ box whole grain elbow macaroni (about 2.5 cups dry)
  • 1 cup canned butternut squash puree
  • ¼ cup + 2 tablespoons evaporated milk
  • ¼ cup chicken or vegetable broth
  • 1 oz low fat cream cheese
  • 1 teaspoon salt
  • ½ cup shredded cheddar cheese
  • 1 tablespoon butter
  • ½ cup onions, sliced thinly
  • 1 large crispy apple, chopped or grated
  • 4 tablespoons crumbled bacon
  1. Heat butter in a skillet over low heat. When melted, add onions and let caramelize for at least 30 minutes for the best flavor. Keep heat on low/low-medium.
  2. Cook the pasta according to directions. Drain and return to pan over low heat. Add butternut squash, chicken broth, evaporated milk, and cream cheese. When combined, add in salt.
  3. Add onions and apples to the pasta. Stir to combine and add a tablespoon more broth or milk if needed.
  4. Just before serving, mix in cheese and stir until melted. Top each serving with 1 tablespoon bacon.
Because there's very little butter, it can "dry out" quickly, especially once off the heat. Add a tablespoon of water, milk, or broth if you need to get it back to its original creaminess.

If this is eating healthy, I like it.

I also like rewarding myself with these cookies afterwards.

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  1. Man, I want to eat pretty much everything that you make. Please can I come and life with you?! I love how you’ve managed to healthy-up this recipe and yet it still looks so delicious.

    • Thanks! But FYI… I don’t post the things that don’t turn out so great. :) It can definitely be hit or miss at our dinner table! And this one was a hit.

  2. Ok, that sounds and looks amazing! Love that it is so healthy, too! The apple sounds like such an interesting but delicious addition.

  3. bookmarked. i REAALLY have to get on the squash mac and cheese bandwagon!

  4. That’s not a pinch of yum…that’s a whole darn SPOONFUL!*

    *Yes, I am as cheesy as I appear. 😉

    I’m going to mull over how I could do a vegan version of this, as I’m in the middle of the Vegan Month of Food. [Otherwise, I’ll save it for when I can have dairy again!]

    • You could totally do this vegan. You could swap some of the milk for a non-dairy milk and you could omit the cheese and cream cheese. And the bacon (boo). Good for you – and good luck! :)

  5. I’ve been seeing a few recipes for butternut squash mac n cheese around the old blog world, but this one looks like the best by FAR!!! Yum!!!

  6. I always love a twist on mac & cheese, this looks so yummy

  7. YES! Love this recipe and will be making it once we are settled!

  8. I love this combination of flavors!

  9. I love:

    1) Your blog
    2) Your photos
    3) The charitable reasons behind why you blog
    4) Your name :smile:

  10. I can’t wait to try this. It looks so cheesy! But healthy enough to make me feel great. :) Thanks for sharing.

  11. Steph Mork says:

    This just reminds fall and it just makes me wanna carve pumpkins and eat macaroni and cheese all day on a day like today! Looks super good!

  12. Reason #153 why I always love to see what you’ve posted. I recently tried pumpkin on pasta and was amazed by it. Butternut squash, cheese, apples, onions? That’s whatever is beyond amazing.

  13. Blog is the New Black says:

    Looks amazing… love that it’s healthified. I made a butternut squash mac & cheese last year, froze some, and recently found it in our freezer… it was still delicious… and it reminded me to make more! 😉

  14. Grammy@gram-cracker.com/blog says:

    My Hubs is a total Mac n Cheese addict, if I sneak this in on him he is either going to divorce me for messing with his favorite dish or love me even more for giving him yet ANOTHER yummy version of his favorite dish….I’ll get back to ya on the outcome!

  15. can I make my own butternut squash

    • Yes, just cook it and puree it. The canned stuff is so quick to use, that’s why I like it. You might also want to use less liquid if you make your own squash as I would imagine it has more moisture.

  16. This looks DIVINE. I will definitely be trying it!! But subbing vegan margarine for the butter, almond milk and I actually have some non-dairy “better than cream cheese” in my fridge! Dairy intolerance will not get in the way!

    • Yeah! Show that dairy who’s boss. :)

      • I’ll be making it this Sunday—and ended up buying butternut squash babyfood to use, as I couldn’t find the canned variety! The ingredients are just pure butternut squash in water, so I don’t see why it wouldn’t work!

  17. I had regular mac-n-cheese on the menu, but it just got voted off the Island. I can hardly contain the drool.

  18. yum yum yum! Looks wonderful and the best fall comfort food!

  19. This is definitely different, but it sounds great! I’m a big fan of butternut squash, and of mac n cheese. So why not combine the two? Thanks for sharing!

  20. No way! Bacon and a good nutritional label?! I’ll be making this for sure!

    • Sadly there’s only one tablespoon per serving. But no one says you can’t make that a heaping tablespoon.

  21. You really took mac n cheese to a whole new level and minus a bunch of calories. You go girl!

  22. Do you cook the apples before putting them in the mix? Or is it just a crunchy delight when you eat? I might try this out for my 10-month old twins…. but they would need the apples cooked, and no bacon (darn, more for my serving then!) If I wanted to cook the apples, would I saute with the onions? Hmmm… Thanks – just found your blog and I think I’ll be a frequent visitor!

    • You can do it either way. If you are worried about it being too chunky, grate the apples! It’s yummy. I also left them raw, and I also sauteed them with the onions. Whatever suits your fancy. :) PS. Can you tell we’ve made it quite a few times??

  23. Lizabeth K. says:

    YUM! I just made my first butternut squash mac and cheese (from the new-ish Cooking Light) and it was SO good. Paul will be upset that I didn’t think to put BACON on it, though! :)

  24. Soo @ Little Miss Fitness says:

    We were just talking about making homemade mac and cheese…now I don’t have to buy a can of Cheez Whiz! :)

  25. Very nice! Going to pick up a butternut squash soon!

  26. What exactly does this taste like? Will picky meat-and-potatos husbands pick up on the squash and apples? Is it conceivable to convince him it’s normal mac n cheese?

    • My husband loved it, but he’s not too picky… if you want to hide the apples a little more, you could grate them instead of chopping!

  27. YAY for squash in pasta! What a scrumptious and healthy recipe, I’d love to dig right in! I bet pumpkin puree would be delish too : )

  28. Ooo, this looks awesome!! I love your cheese strands in the photo :)

  29. I prepared this yesterday and it was delicious. Thank you for the recipe!

  30. I made this for dinner tonight- it was awesome! I couldn’t find pureed butternut squash, so I subbed sweet potato puree and it still worked.

    • Me too! I make it at least once a week. :) I’m glad you liked it! Bummer about the butternut squash puree… but sweet potato would be tasty, too!

  31. I have been eyeing this recipe for a few weeks now and made this Friday night for my family and Wow- everybody loved it! Absolutely delish! All of the flavors just compliment each other so well. I made a double-batch w/ zero leftovers :)

  32. Living The Sweet Life says:

    I think in another life, we MUST have been best friends or something …. ” I have a thing for secretly healthy things that don’t seem healthy.” ME TOO!! I love this recipe. I’ve never tried butternut squash mac & cheese – – but clearly I live in a box :(

  33. Do you cook the apples with the onion or leave them uncooked?

  34. I made it last night!!! It was soooo good!!! I have already shared it with everyone and I can’t wait to make it again! I made my own puree for the butternut squash and it was so good! I used honey, orange zest, butter and salt and pepper to taste! Thank you again for your creativity!

  35. I was a skeptic….but this ROCKED! I’m sharing it on my Facebook page. Yummo!

  36. I’m sorry, I really wanted to like this, but the combination was just too sweet for mac and cheese.

    • Shoot – sorry you didn’t like it. Maybe you could try omitting the apples? Otherwise I’ve seen lots of recipes for spicy mac and cheese lately; maybe that would be more up your alley!

  37. Kaylee Bosworth says:


  38. I just discovered your blog today and I think I’m in love! I like it here and I really really like this mac and cheese. This will be gracing my table in the very near future. So glad to have found you!

  39. This really does look delicious. I’ll bet it gets a thumbs up from the hubs next week!

  40. Beautiful blog and great photos!!!

  41. This looks amazing and I reallyyy want to make it but I’m having trouble finding butternut squash puree. I live in London and they just don’t seem to have it anywhere. Would pumpkin puree work just as well to avoid having to make butternut squash puree myself? I happened to find some of that at Whole Foods.

    • Lindsay says:

      Ok, so there are two options. One – make it with the pumpkin, which will be similar to this: http://pinchofyum.com/healthy-bacon-pumpkin-pasta, or two – buy a whole squash, cut it up, cook it, and puree it yourself. I would go with the pumpkin. I actually like the delicate taste of squash better, but for the sake of convenience, I think pumpkin is a great choice. :)

      • Thanks Lindsay! I also saw your bacon-pumpkin-pasta which looks delicious as well! I might go for the pumpkin first then when I’m not feeling so lazy make the butternut squash puree myself. :)

  42. I tried this recipe this evening for my husband and I (it seemed like adult mac & cheese), and I was’t sure how he’d like it. [He’s not a veggie eater] But, he LOVED IT! So, thanks for the recipe! If I can get it past my hubby my toddler will like it too. :)

  43. Can you suggest a substitution for the evaporated milk?

  44. Lindsay, I have been rumaging thru low cal cookbooks lately try to make some lifestyle changes in my older years (64). While I am currently avoiding pasta, even whole grain, I appreciate the effort you put into this to make it healthier. I may give it a try and substitute spagetti squash for the pasta. Let you know how it turns out!

  45. I love using rice pastas. They are usually one ingredient (rice) and come in all different shapes and sizes. A great alternative to wheat pasta.

  46. Just found your website and lovvvvvvve your recipes! Thanks for all the yummy food ideas!

  47. This recipe reeeaaaaalllly makes me crave FALL!

    • Funny – I thought the same thing the other day! I was having a flashback to this recipe. But I won’t be getting fall for a looooong time (Filipino seasons are hot, hot, hotter, and hottest). :)

  48. Oh my, this is going on my fall to-make list immediately! Awesome combination of flavors!

  49. Um … incredible!

  50. I’m going to try this with some hot sausage mixed in instead of bacon on top, and with gluten free macaroni and soy milk!

  51. Would love to try this because I have butternut squash from the garden. As a replacement for the canned puree…any idea how much fresh squash I’d need? I can puree it in the food processor but I wasn’t sure if half a cup of fresh was equal to half a cup canned.


    • Yeah, I think they’d be about equal. The canned kind is really dense so is just go easy on the liquid when you purée it to keep it a similar density. :) how cool that you grow squash! Love it.

  52. I’m planning on making this for my lunch for the work week, should I wait to add the cheese until serving it daily, or add it and thanks! I’m excited to make this dish.

    • It works fine to add it in ahead of time, but it’d probably be nice and gooey if you waited to put it on right before serving. :) Hope you like it as much as I did!

  53. This is fantastic… I woke up knowing my squash would be put to good use. This is a hit- I topped it with some brown sugar and this easily is a dish I will make again! I’m now very excited to read more of you ‘Pinches of Yum’ that I can recreate!

  54. This was very good!!!! The bacon brought all of the tastes together beautifully!

    (But please change the prep time! Not counting the time I had to roast & mash the squash, this took about an hour to prepare! Chopping onions, apples, cooking onions & pasta, mixing, etc…)

  55. I saw this recipe floating around the web soon after you posted. I was skeptical. Squash Mac and Cheese?

    Then I saw the pictures. I am 100% convinced. That. looks. incredible.

  56. This looks divine!

  57. Made this for dinner tonight & it was really good! I left out the bacon though because I didn’t have any, but I wish I put it in!

  58. The squash macraoni and cheese was wonderful!! Very creamy. Made great reheats with some added leftover chicken broth or evaporated milk! Will be making this recipe again!!

  59. I found your blog only recently, and even though you posted this recipe a year ago, I am compelled to comment. I made it for tonight’s dinner and it is delicious! Even my ten month old daughter loves it. When she finished the portion I gave her for supper, she cried for more! I haven’t discovered many foods that get that kind of response from her. This is a make-again for sure.

  60. Made this for dinner tonight and it was a hit :) The kids weren’t super fond of the carmelized onions so i think next time I might puree them up with the squash as they added a really nice flavour. So creamy and yummy, will be making this again for sure!

  61. My local grocery store isn’t so good…Do you think I could use canned pumpkin instead of the 1 cup of butternut squash puree?

    • I do! :) Or you could puree your own. I didn’t used to do that in the States because I had it readily available and I liked the canned stuff fine, but here in the Philippines I can’t find it, so I always puree my own and it’s really really good!

  62. Felicity says:

    I pinned this on pinterest a while ago, and tonight I finally made it!
    Except I had to put my own spin on it due to lack of ingredients. The variation I made was AH-MAZING though, and my partner had a second helping within minutes of gobbling down his first. I thought I would share with you what I did – since it was your delicious recipe that was my inspiration in the first place :-).
    I substituted pumpkin soup for roasted pumpkin cubes with a drizzle of maple syrup, and I made a traditional white cheese sauce.
    I incorporated some chicken stock that I cooked the pasta in, in with the cheese sauce and used a lil mozzarella into the cheese sauce along with edam cheese.
    Some of the roasted pumpkin became mashed up a bit when I stirred all the ingredients together at the end, and some pieces stayed as the cubes. It made the cheese sauce a slight orange colour like yours.
    All in all I think I have just found an exciting new take on macaroni and cheese!
    So thank you for your recipe!

  63. Elizabeth Shatz says:

    I really liked this recipe and would have given it 4 stars, however I think the nutritional information is off. Using 2 1/2 cups of whole grain pasta alone is 1100 calories which comes to 275 calories per serving based on 4 servings. How did you calculate the nutritional information? I used Barilla whole grain pasta. Half box doesn’t come to 2 1/2 cups….that amount is much more than half the box.

  64. I made this tonight and it was SO GOOD!! My 10 month old couldn’t eat it fast enough!

  65. I just made this and OMG…It’s amazing!! The BEST Mac and Cheese I EVER had…2 thumbs up <3

  66. Great Mac and cheese. Thank you.

  67. Jessica Ford says:

    This looks SO good! I love butternut squash. I can’t wait to try this.

    • Jessica Ford says:

      I didn’t have time to get butternut squash at the store today, so I made it with pumpkin instead. It was pretty good, although not as cheesy/gooey as your picture. My husband and I liked it, but my kids weren’t crazy about it. I think I’ll definitely try it with butternut squash too. I made homemade pumpkin beer bread, recipe courtesy of Gimme Some Oven. It was a yummy, pumpkin meal!

  68. Oh my word, made this for dinner last night and it was awesome!

    Not gonna lie, I just scooped out some squash I had roasted and didn’t bother pureeing… it was perfect, anyway.

    We had dinner with friends who have a VERY fussy 8-year old with a major aversion to anything squash… he had two servings and loved it… we finally told him there was squash in it and he almost fainted. Haha!

    Thanks for a great recipe!!!

  69. This was dynamite! I did sub in pumpkin for squash, and added balsamic to my onions (which I doubled, because we love them) as they caramelized. Also, a couple healthy cranks of black pepper at the end. Soooo good. Tasted like something you’d get at a 5-star restaurant and nothing like the stuff in the blue box, which is a double win for our house!

  70. I couldn’t find the puree so I am making my own. Question though… Do I season the puree or leave it plain? I don’t know if the canned puree has seasoning. Making tonight so a response would be awesome! Thank you so much

  71. Made this recipe tonight.. It was delicious! I added walnuts instead of bacon and it was amazing

  72. Viktorija Gorcakovaite says:

    OMG, I subscribed here thinking that you’re vegan as I found so many nice recipes… Sad to find out that you’re not. Unsubscribed.

  73. Heather says:

    I made this for dinner last night and it was awesome! I made a couple of additions for fun… I added about 1/2 cup of applesauce to the butternut squash, and I sautéed up some chicken apple sausage to add to it. It reminded me of Thanksgiving! It was delicious! I also added a little but of greek yogurt at the end just to make it a little creamier. I think it helps it not “dry out” as much the next day, as I just had some for leftovers and it was really creamy. Thanks so much for the awesome recipe! I love your blog :)

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  97. stephanie says:

    Omg, I have to make this! Your pictures are to die for! Question…I make “pasta” out of butternut squash. Would this sauce be too much of the same, do you think?

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  108. Meghan Jefferson says:

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