Skinny Double Chocolate Chip Muffins.

You will not even realize these double chocolate muffins are lightened-up and low fat!

Skinny Double Chocolate Muffins from You will not even realize these double chocolate muffins are lightened-up and low fat!

I know, I know.  I make skinny muffins all the time. And yes, I’m sharing another recipe with you today.  But can you blame a girl?  I love muffins and making them a teensy bit healthier is just so easy to do. I love freezing them for later, grabbing them on the go out the door to work, and snacking on one after I get home. They are just so convenient and I never feel guilty digging in.

Sally’s Skinny Muffin Addiction.

And today’s muffins are totally acceptable for dessert, too. Double chocolate, anyone?

Skinny Double Chocolate Muffins from You will not even realize these double chocolate muffins are lightened-up and low fat!

I made these muffins twice last weekend. I developed the recipe as I went. Sometimes the best of recipes just come to me as I’m mixing the whole wheat flour and baking soda together. Other times I have recipe fails, other times I lay in bed and scribble down ideas as I’m falling asleep. All Day I Think About Recipes.

I woke up one morning with no plans at all the make healthy double chocolate muffins – they sort of just happened. And we loved them so much, I made a second batch the next day to freeze.  I brought a couple into work and no one could tell that they were healthified.  Kevin said the same:

“What is this you’re giving to me?”

It’s healthy.

“No it’s not.”

Healthy recipes that don’t taste healthy at all are like finding gold.

Skinny Double Chocolate Muffins from You will not even realize these double chocolate muffins are lightened-up and low fat!

Today’s healthy chocolate miracle muffins are insanely easy to make. Start with some of your wet ingredients: unsweetened applesauce, some sugar, and honey.  Applesauce is taking the place of butter and oil in this recipe; there is simply no need for the added fat.  Sometimes healthy baked goods without the presence of fat can be dry and crumbly.  I can’t stress enough that these are NOT anything like that.  The applesauce and a few other ingredients in the recipe do a fine job keeping the baked muffins moist, tender, and soft.

There is only 1/2 cup of white sugar in the whole recipe, yielding 12 large muffins. 1/2 cup of sweetener is not enough, so I added 1/4 cup of honey as well.  Honey sweetens my Skinny Banana Blueberry Muffins too.  I love the stuff.  A few more wet ingredients are egg whites, greek yogurt, and vanilla extract.  Instead of using 1 egg, I used two egg whites to keep the fat count low. Just like the applesauce, the greek yogurt does a fine job keeping the muffins moist and negating the purpose for added fat like butter or oil. I used fat free vanilla greek yogurt, but feel free to use regular yogurt – either low fat, fat free, plain, or vanilla flavored.

Greek yogurt keeps my Skinny Chocolate Peanut Butter Swirl Cupcakes insanely moist and decadent tasting!

Skinny Double Chocolate Muffins from You will not even realize these double chocolate muffins are lightened-up and low fat!

The dry ingredients are simple: all-purpose flour, whole wheat flour, unsweetened cocoa powder, and your leavening agents.  You will use 1/2 cup of both flours and the cocoa powder, which I loved.  It’s so easy to remember!  You may sift the dry ingredients together, which I did, but this step is not necessary.  Sifting gets rid of any cocoa powder crumbles, making it easy to mix with the other ingredients in the recipe.

The last thing you’ll add? Chocolate chips of course!  I used mini chocolate chips.  I find that mini chocolate chips gave me more chocolate chip/muffin ratio.  Chocolate chips in every bite for the same amount of calories.  I’ll take it!  Feel free to use regular size, or leave them out completely.  I will warn you though: leaving the chocolate chips out will prevent you from enjoying how melty they get inside the muffin after you warm them up in the microwave. Trust me – biting into a warm muffin, filled with melty chocolate chips, and knowing that it is healthy is like heaven on earth!

Mini Chocolate Chips

The cupcakes take an easy 18 minutes in the oven.  Similar muffin recipes of mine took 20 minutes in my last oven, so I would say anywhere between 18-20 minutes.  Be careful with these though – you don’t want to overbake them, which will lead to a dry, course muffin. It’s hard to tell when they are overbaked since they are all chocolate brown; insert a toothpick in one at the 18 minute mark. If it comes out clean, they are ready. If not, bake for 2 more minutes.

I will warn you: do not use cupcake liners for these muffins. The muffins will stick. Sadly, I know from experience. The smell of chocolate muffins baking in your kitchen is simply unparalleled. Your kitchen has just turned into a bakery and the only thing on the menu is chocolate! Chocolate for breakfast is always a good thing in my world.

Skinny Double Chocolate Muffins from You will not even realize these double chocolate muffins are lightened-up and low fat!

Today’s muffins are the perfect healthy recipe. No mixer required, taking 10 minutes to prepare the batter, and are made with so many easy ingredients: greek yogurt and applesauce keep the muffins moist and soft, they are sweetened with only a little sugar and honey, made with whole wheat flour, and practically calorie-free unsweetened cocoa powder.

And mini chocolate chips. Always mini chocolate chips, people. They taste completely sinful – eating one completely feels like you’re cheating.  Again, no one knew these were healthy when they tried one! Sneaky little muffins, aren’t they? Wait until you try one warm and melty from the oven!! Ok, I’m done convincing you. Make these!

Follow me on Instagram and tag #sallysbakingaddiction so I can see all the SBA recipes you make. 

Skinny Double Chocolate Chip Muffins

Yield: 12 muffins

Print Recipe

You will not even realize these double chocolate muffins are lightened-up and low fat!


  • 3/4 cup (133g) unsweetened applesauce
  • 1/2 cup (100g) granulated sugar
  • 1/4 cup (85g) honey
  • 2 large egg whites (or 1 large egg)
  • 3/4 cup (183g) vanilla Greek yogurt (or regular yogurt, plain or vanilla)
  • 2 teaspoons vanilla extract
  • 1/2 cup (62g) all-purpose flour (measured correctly)
  • 1/2 cup (64g) whole wheat flour (measured correctly)
  • 1/2 cup (42g) unsweetened cocoa powder
  • 1/2 teaspoon salt
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/2 cup (90g) mini chocolate chips, plus a few more for sprinkling on top


Preheat oven to 425F degrees. Spray 12-count muffin pan with nonstick spray. Do not use liners.

In a large bowl, combine applesauce, sugar, honey, egg whites, greek yogurt, and vanilla extract. Whisk them all together until smooth, with no yogurt lumps remaining.

Sift* the flours, cocoa powder, salt, baking soda, and baking powder together. Slowly stir in the wet ingredients, being careful not to overmix. Get any dry pockets of flour out. Fold in the mini chocolate chips. The batter will be a little chunky. This is ok.

Divide the batter evenly among the muffin cups - fill them all the way to the top if you can. Bake for 5 minutes at 425F. Keeping the muffins in the oven, reduce the temperature down to 375 and continue to bake for 13 more minutes. Insert a toothpick into the center of one muffin. If it comes out clean, they are done. If not, bake for only 2 more minutes.

Remove from the oven and allow to cool for 3 minutes in the pan, then transfer to a wire rack to cool completely. Makes 12 muffins. Muffins stay fresh in an airtight container at room temperature for up to 5 days. Muffins freeze well up to 3 months: heat up for 45 seconds to thaw.

Additional Notes:

*Sifting the dry ingredients is optional.

*Why the initial high temperature? See my sky-high muffin dome tricksfor more detail.

© Sally’s Baking Addiction. All images & content are copyright protected. Please do not use my images without prior permission. If you want to republish this recipe, please re-write the recipe in your own words, or link back to this post for the recipe.

You will also love these Skinny Strawberry Chocolate Chip Muffins!

Skinny Strawberry Chocolate Chip Muffins


See more healthy recipes.

See more healthy muffin recipes.


357 Responses to “Skinny Double Chocolate Chip Muffins.”

  1. #
    Courtneyposted April 3, 2015 at 3:23 pm

    These look delicious! Could i make these in a 9×13 pan? How long and what temp would you bake them at?


    • Sallyreplied on April 3rd, 2015 at 7:15 pm

      To make a cake of sorts? I don’t think there is enough batter for a large pan. Maybe a 9×9 pan. I would bake it at 350 and I am unsure about the time.


  2. #
    Jennyposted April 3, 2015 at 4:57 pm

    These are amazing! Finally, a skinny muffin that tastes nothing like a skinny muffin! Perfect texture and flavor! Thank you! :)


  3. #
    Michelleposted April 7, 2015 at 12:20 am

    I love these muffins! They are so delicious and easy to make! My step daughter (who loves all things junk food and is addicted to Costco muffins) thought these were amazing and wants to help me make them next time! That’s a serious win


  4. #
    Courtney Shorrposted April 9, 2015 at 12:07 pm

    I know it’s been almost a year since you posted this but I HAD to leave a comment. I made these today with my 2, 4, and 6 year old kids and they were a MAJOR HIT! They loved them and I felt ok letting them eat another because of how healthy everything was! My only substitute was I used plain greek yogurt because I didn’t have vanilla greek yogurt…. but it turned out PERFECT. Moist and Delicious without being over sweet. I am amazed by this recipe! Bravo!


  5. #
    Meganposted April 15, 2015 at 4:33 pm

    Can you make 6 jumbo muffins instead of 12 regular sized ones?


    • Sallyreplied on April 15th, 2015 at 4:50 pm

      Absolutely! I’m unsure of the bake time.


  6. #
    Marlaposted April 17, 2015 at 10:05 am

    OMG these are sooo good thank you Sally!!!


  7. #
    Beckyposted April 18, 2015 at 4:46 pm

    Hi Sally! Any chance these can be made into a cake? How would that go in terms of timing/temp? Thanks!!


    • Sallyreplied on April 19th, 2015 at 8:38 pm

      Yes! Use a 8 or 9 inch square bake pan – at 350F – around 30-34 minutes.


  8. #
    UmHudeposted April 28, 2015 at 9:22 am

    These sounds delectable!!! Can’t wait to try these! Can the flour be substituted for GF flour like almond or coconut??? Can’t use barley/bran/flax type stuff either :-(
    Tried the cranberry orange muffins and they were TO DIE FOR!!! a friend shared your recipe and we’ve made them everyday since!!! THANK YOU!!!!
    Um Hude


  9. #
    janeposted May 14, 2015 at 11:37 am

    Just made these.  They are wonderful ! !!!!!


  10. #
    Victoriaposted May 18, 2015 at 11:06 am

    I have made these numerous times and I love these. They don’t taste healthy at all! Two things I would recommend for readers is avoid Dutch-processed cocoa powder (the “dark chocolate” cocoa powder); I like to default to this kind, but it made the muffins taste too rich and over-flavored. Second, I would recommend NOT substituting oil for applesauce! Please, spend the couple bucks to get applesauce instead. Oil does not ruin how the muffins turn out, but it makes them taste so greasy.


  11. #
    Elaineposted June 10, 2015 at 9:07 am

    Why do you not respond to the questions being asked about the calories or nutritional value in your recipes.


  12. #
    Jamieposted June 15, 2015 at 11:49 am

    My boys keep asking for McDonalds double chocolate muffins so I thought I’d try a substitute with these and they are GREAT! One batch was not nearly enough for my four boys and the neighbor boy, lol. I will use full fat yogurt and the whole egg to try and fill the boys up a bit better. But these were so good!


  13. #
    Rebeccaposted July 12, 2015 at 11:46 pm

    What can I use as a non dairy substitue for the yogurt? Will a Fat free non dairy creamer work? Thanks!!


  14. #
    JTposted July 25, 2015 at 1:28 pm

    Hi Sally, I have been on the hunt for a low fat, yet delicious chocolate muffin recipe and I must say I am quite pleased with how they taste. It almost felt like I was eating a regular chocolate cake. I substituted white sugar for brown sugar and it still tasted great.

    I do have a question though. You see, getting Greek yoghurt (or plain yoghurt in general) where I live is close to impossible and when I do find it, the price does not encourage me to buy it. I’d substitute for sour cream but finding that is just as impossible (in most case when I need it, I make my own sour cream but it is full-fat). Also, finding buttermilk….well, I won’t repeat myself again (lol)

    For this recipe, I used semi-skimmed milk and obviously it did not come out “muffin-like” as it made the wet to dry ingredient ratio was completely off. Even I could tell it would be before I tested the recipe. If I don’t find yoghurt, would you advice I reduce the amount of milk and if so, by how much? Thanks


    • Sallyreplied on July 27th, 2015 at 3:25 pm

      Try reducing the milk by 2 Tablespoons. This tiny amount may help!


  15. #
    Michelleposted August 2, 2015 at 5:00 pm

    hi made these today and they are sooooo good! They satisfy my chocolate craving (and that is very hard to do!) thank you for the recipe!


  16. #
    Robinposted August 8, 2015 at 3:34 pm

    Hi Sally,
    I have made these muffins numerous times and are by far my favorite healthy muffin recipe. I was curious, would it be possible to sub flour or something non-cocoa for the cocoa to turn it into a regular muffin base appropriate for adding fruit or chocolate chips? I like the combo of applesauce and yogurt in this particular recipe.


    • Sallyreplied on August 9th, 2015 at 6:03 pm

      Flour is not a sub for cocoa powder in this recipe. Try this muffin recipe as the base instead!


  17. #
    Luanneposted August 14, 2015 at 11:52 am

    Hi Sally, I have most of the ingredients except for applesauce and honey. Can I sub applesauce and honey with mashed banana? Or banana for applesauce and additional sugar for honey? How many maybe? Thanks you! Hope to hear from you!


  18. #
    Camelliaposted August 24, 2015 at 10:31 am

    Can I use unsalted butter instead of non-stick spray? Non-stick spray is not readily available where I’m from. Weird, I know.


    • Sallyreplied on August 24th, 2015 at 3:11 pm

      You can grease the muffin pan with butter, yes.


  19. #
    Leanneposted August 30, 2015 at 2:03 pm

    I made 2 batches of these yesterday and am truly impressed! The muffins are delicious and you can’t tell they are a healthier version of what would normally be a very unhealthy muffin. Thanks Sally, for providing a healthy option that I am happy to give to my family. This recipe is a definite keeper! I can’t wait to try your other healthy muffins.


  20. #
    Heatherposted August 31, 2015 at 11:47 am

    I made these last night and they are fantastic!
    I used extra dark cocoa powder but maintained everything else as instructed and they are so moist and delicious!

    I will make them again.


  21. #
    rudiposted September 15, 2015 at 3:54 pm

    What is the exact nutritional info?


  22. #
    Devikaposted October 2, 2015 at 2:30 am

    Hi, what would be the temperature requirement and the time for each stage for mini muffins?


  23. #
    Toriposted October 11, 2015 at 8:44 am

    Really wonderful muffins, so lovely an moist! I used Balkan-style plain yogurt in place of Greek yogurt, but they’re basically interchangeable:) Only complication I ran into was sifting the dry ingredients, all the thicker wheat pieces from my whole wheat flour got sifted out, so I tried to grind them finer and get some more of it in, but alas, proved too time consuming to keep doing so I chucked the last little bit out.

    ANYWAY, that’s very minor, and these muffins are some of the moistest, most chocolatey muffins I have ever had, they’re just wonderful. And if anyone else is wondering, they’re 5PP on Weight Watchers when made with egg whites.

    Thanks for the great recipe! Saved me in a pinch when the zucchini for my zucchini chocolate muffins fell through!


  24. #
    Toomsposted October 27, 2015 at 7:37 am

    Oya oyaaa i LOVE these muffins
    I can’t believe they don’t have any butter although I made them myself!

    Everyone is asking me how many calories are in these pieces of heaven and I don’t know!! 

    Thanks Sally for the recipe


  25. #
    Laurenposted October 27, 2015 at 11:09 am

    These are out of control delicious! Finally a healthierchocolate recipe that doesn’t lack in flavor! 


  26. #
    Natalieposted November 12, 2015 at 6:33 pm

    I made these muffins today and they are fantastic!!!!  I followed the recipe exactly and they turned out great.  This is a quick and easy recipe!! Thank you!!!!


  27. #
    Ellenposted November 17, 2015 at 12:54 pm

    I would like to try this recipe, looks delicious and healthy. I have all ingredients except whole wheat flour.   Is there anyway I can do without or use more regular flour ? Thanks!


    • Sallyreplied on November 17th, 2015 at 2:41 pm

      You can use all all-purpose flour.


      • Ellenreplied on November 17th, 2015 at 3:01 pm

        So would I substitute all purpose flour for whole wheat or just disregard the whole wheat part?

  28. #
    Jodiposted November 22, 2015 at 9:34 am

    These are so delicious! My son called them “a brownie in muffin form” They were all gone before I could get any in the freezer to save for school lunches! And that is why I’m pulling the ingredients out for the second time in two days.  I was sceptical, but I even used the initial high heat, and they turned out beautifully!


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