Butternut Squash Mac and Cheese with Caramelized Onions, Bacon, and Apple Recipe - Skillful Cook
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Butternut Squash Mac and Cheese with Caramelized Onions, Bacon, and Apple

33 reviews / 4.8 average

I have a thing for butternut squash mac and 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. 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 and cheese with caramelized onions, crispy bacon, and fresh sweet apples on a fork.
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A picture of <span class="fn">Butternut Squash Mac n' Cheese with Bacon, Caramelized Onions, and Apples

Butternut Squash Mac n' Cheese with Bacon, Caramelized Onions, and Apples


This healthy butternut squash mac and cheese has caramelized onions, crispy bacon, and fresh sweet apples. It's my go-to comfort food!


  • 1/2 box whole grain elbow macaroni (about 2.5 cups dry)
  • 1 cup canned butternut squash puree
  • 1/4 cup + 2 tablespoons evaporated milk
  • 1/4 cup chicken or vegetable broth
  • 1 oz low fat cream cheese
  • 1 teaspoon salt
  • 1/2 cup shredded cheddar cheese
  • 1 tablespoon butter
  • 1/2 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.

  • Prep Time: 30 mins
  • Cook Time: 20 mins
  • Category: Dinner
  • Cuisine: American

Keywords: healthy butternut squash mac and cheese, healthy mac and cheese, squash mac and cheese

If this is eating healthy, I like it.

I also like rewarding myself with these cookies afterwards.

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  1. Skillful Cook Logo

    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!]

    1. Skillful Cook Logo

      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! 🙂

    1. Skillful Cook Logo

      Aw thanks! I first made butternut squash mac and cheese last year and fell in love immediately.

    1. Skillful Cook Logo

      This is a housewarming recipe to remind you of the fall days back in MN. 🙂 Hope the move is going well!

  2. Skillful Cook Logo

    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.

    1. Skillful Cook Logo

      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.

  3. Skillful Cook Logo

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

  4. Skillful Cook Logo

    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!

    1. Skillful Cook Logo

      Carving pumpkins! You should come to our house and carve pumpkins and eat macaroni and cheese some weekend. Wanna??

      1. Skillful Cook Logo

        YES! Sounds like a treat 🙂 I have a long weekend coming up so I will be home anyways, maybe I’ll have to make a trip over 🙂

  5. Skillful Cook Logo

    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! 😉

  6. Skillful Cook Logo

    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!

    1. Skillful Cook Logo

      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.

  7. Skillful Cook Logo

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

    1. Skillful Cook Logo

      Exactly. Not too much cheese, but enough to make it gooey and melty and wonderful.

  8. Skillful Cook Logo

    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!

      1. Skillful Cook Logo

        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!

        1. Skillful Cook Logo

          Bummer – I can usually find some in the beans and canned veggies section! Hope it works out! 🙂

          1. Skillful Cook Logo

            I live in a big Canadian city but canned butternut squash doesn’t seem to be a thing here! All canned pumpkin 🙂
            We make this recipe regularly at my house and I roast a butternut squash and then blend it with the evap milk. Makes for a super creamy sauce!

  9. Skillful Cook Logo

    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.

    1. Skillful Cook Logo

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

        1. Skillful Cook Logo

          So glad you liked it! It’s my new favorite winter-cozy-still-kindof-light meal. 🙂

  10. Skillful Cook Logo

    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!

    1. Skillful Cook Logo

      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??

  11. Skillful Cook Logo

    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! 🙂

  12. Skillful Cook Logo

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