Skinny Chocolate Peanut Butter Cupcakes

Lightened-up chocolate cupcakes made from Greek yogurt, whole wheat flour, bananas, cocoa powder, and not much else! Frosted with a little peanut butter swirl. You’ll have no idea they’re skinny!

chocolate peanut butter cupcakes topped with peanut butter chips

Another peanut butter and chocolate recipe for you today. I have no shame!

Today I’m sharing a skinny version of a chocolate cupcake. Filled with dark chocolate chips, swirled with peanut butter, and topped with peanut butter chips. This recipe was born from my Skinny Chocolate Banana Fudge Muffin recipe. I replaced all of the applesauce and some of the banana with creamy 0% plain greek yogurt. I added a generous dash of vanilla extract and replaced the egg with 2 egg whites. These cupcakes are full of protein packed ingredients – about 6 grams of protein per cupcake, which is impressive for a cupcake.

*Feel free to plug the ingredients into an online calorie counter to get the full nutrition stats.

The cupcakes have whole wheat flour, no butter and no oil, and only 1/2 cup of sugar for the whole recipe – not bad at all for dessert. Feel free to leave out the chocolate and peanut butter chips to reduce the sugar even more. I loved how the chocolate chips got all melty inside, so I don’t think I’ll ever cut those from the recipe. 😉

hand holding a chocolate peanut butter cupcake topped with peanut butter chips

Now, I’ve had readers tell me that just because there is no butter or oil in some of my recipes, that doesn’t make them healthy. However, I firmly believe that chocolate is good for the soul, protein is necessary for our fabulous thigh muscles, and the peanut butter keeps our hair, skin, and smiles glowing. I’m so corny, I know.

Which is why I’m labeling this dessert cupcake as skinny – it’s a lightened up version of a traditional chocolate cupcake, made with more nutritional alternatives. 🙂

Let’s dig a little deeper into how you can make them.

chocolate peanut butter cupcakes topped with peanut butter chips

The first step is to mix your wet ingredients together. The wet ingredients are 0% plain greek yogurt, 2 egg whites, 1/2 cup sugar, vanilla extract, and 2 large bananas. Feel free to use a vanilla flavored yogurt instead. I do not recommend reducing the sugar because there is so much cocoa powder in the dry ingredients that your cupcakes may taste bitter. Make sure your bananas are extra ripe. Mine had been dying on the counter for several days. The riper, the better (I cannot stress this enough!). Also, you may use 1 full egg instead of egg whites if you’d like.

I wanted to keep the banana taste down to a minimum, so that the focus is mainly on the chocolate and peanut butter. I made a test recipe on Saturday and used 1.5 cups of mashed banana (about 3 large bananas) and brought them to my friends. While certainly tasty, they said, the banana taste was strong. I made the cupcakes again on Sunday and reduced the mashed banana to 1 cup (about 2 large bananas) and replaced the extra moisture with greek yogurt.

The greek yogurt and mashed bananas make for some very moist and soft cupcakes. I find that dessert items without butter or oil tend to be very dry. That is SO not the case with these. Some of my friends were in shock when I told them that the recipe is full of healthier substitutes.

chocolate peanut butter cupcakes topped with peanut butter chips in a cupcake pan

Once you mix up all of the wet ingredients, you may be surprised at the volume of it all. You did nothing wrong – there is supposed to be a lot of wet ingredients to soak up all of the flour and cocoa powder.

The dry ingredients used are a mix of all-purpose and whole wheat flours, unsweetened cocoa powder, salt, baking powder and baking soda. I steered away from using strictly whole wheat flour in the cupcakes because I didn’t want them to taste heavy – more like a cupcake, less like a muffin. Feel free to use all whole wheat flour or even white-whole wheat flour (I was all out).

There is a whopping 1/2 cup of cocoa powder in this recipe. That makes for some intense fudgy cupcakes. I love using unsweetened cocoa powder in healthy recipes – you get chocolate flavor for hardly any calories. I always have a couple containers of Hershey’s Special Dark in my pantry.

An important note: try to sift the dry ingredients together. Cocoa powder is full of lumps and the last thing you want are pockets of dry cocoa powder when you bite into your finished cupcake. I always sift my cocoa powder when a recipe calls for it. With sifting, you will still measure the amounts of the dry ingredients in the recipe, then sift them together. If you do not own a sifter, whisk the dry ingredients together VERY well to get all of the lumps out.

chocolate peanut butter cupcakes topped with peanut butter chips

Slowly mix the wet ingredients into the dry ingredients. Gently mix it up with a large spoon or rubber spatula. No mixer is required! Make sure you get all of the pockets of cocoa powder and flour out of the batter, there may be some hiding at the bottom of the bowl.

When it comes to mixing this batter, I like to think of it as “less is more.” Go for the least amount of mixing possible to combine the wet and dry ingredients.

Gently fold some dark chocolate or semi-sweet chocolate chips into the batter. These are optional, but I have to tell you how unbelievable the melty chocolate chips inside taste. Even when the cupcakes have cooled, the chocolate chips still stay soft and melty; they don’t harden up much at all.

Divide the batter between 12 cupcake liners. You want every last drop of this batter, so scrape that bowl clean. PS: good luck not tasting the batter. It tastes like brownie batter.

Ok, so you may be asking me… where’s the frosting? No cupcakes are complete with frosting! Well, to keep the cupcakes on the lighter side, I used a thick peanut butter swirl as the frosting and topped them with peanut butter chips. In my world, if peanut butter and frosting had a battle, I’m not sure who would win. I have an equal affection for both.

So peanut butter = frosting in this recipe. And you don’t see me complaining.

chocolate peanut butter cupcake batter in a cupcake pan

Melt 1/4 cup of creamy peanut butter (or use runny natural peanut butter) and spoon 1 teaspoon of it onto each cupcake. Using a knife or a toothpick, gently swirl it around into the batter. Top with peanut butter chips.

There’s a double dose of peanut butter here and I like it.

stack of 2 chocolate peanut butter cupcakes topped with peanut butter chips

chocolate peanut butter cupcakes topped with peanut butter chips

The cupcakes take about 20 minutes in the oven. Try with all of your self control to wait until they cool before unwrapping and eating one. That didn’t go over so well with me – I mean, I could hardly wait an extra minute when I pulled them out.

You will never, ever guess that these dessert cupcakes are made with good-for-you ingredients like bananas, whole wheat flour, egg whites, and greek yogurt. They are so rich in chocolate flavor that you’ll think you are eating a brownie. The thick creamy peanut butter swirl and peanut butter chips give each bite that little something extra. The texture is moist, fluffy, and soft like the best chocolate cake you’ve ever had.

It will be love at first chocolatey bite.

chocolate peanut butter cupcakes topped with peanut butter chips

Let’s not forget about how EASY and quick this recipe is. There are no strange ingredients requiring a trip to a specialty grocery store – the ingredients are convenient and normal. The batter is mixed by hand in about 5-10 minutes and the cupcakes take about 20 minutes in the oven.

And it will take you only about 30 seconds to polish one off. And if all of this wasn’t enough, the best part about this recipe is that you are not sacrificing taste or convenience for a lightened up chocolate peanut butter cupcake.

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

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chocolate peanut butter cupcakes topped with peanut butter chips

Skinny Chocolate Peanut Butter Swirl Cupcakes

  • Author: Sally
  • Prep Time: 20 minutes
  • Cook Time: 20 minutes
  • Total Time: 1 hour, 30 minutes
  • Yield: 12 cupcakes
  • Category: Cupcakes
  • Method: Baking
  • Cuisine: American


These dessert cupcakes are made with healthier alternatives and ingredients that are convenient and easy. No trips to a specialty grocery store. They are unbelievably fudgy, with subtle banana flavor, and a thick swirl of peanut butter as the frosting. They have 6 grams of protein each; full nutrition information available by visiting a calorie counting website and plugging in the ingredients.


  • 2 large *very* ripe bananas, mashed (about 1 cup – the riper, the better)
  • 1/2 cup granulated sugar
  • 2 large egg whites
  • 3/4 cup Greek yogurt
  • 2 teaspoons pure vanilla extract
  • 1/2 cup whole-wheat flour (spoon & leveled)
  • 1/2 cup all-purpose flour (spoon & leveled)
  • 1/2 cup unsweetened cocoa powder
  • 1/2 teaspoon salt
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 1/2 cup semi-sweet or dark chocolate chips
  • 1/4 cup creamy peanut butter, melted
  • optional: 1/3 cup peanut butter chips


  1. Preheat the oven to 375°F (191°C). Line a muffin tin with baking cups. Set aside.
  2. In a large bowl mash the bananas with a fork or use a hand mixer. Mash them very well – no big lumps. Stir in the sugar, egg whites, greek yogurt, and vanilla extract.
  3. Sift* the flours, cocoa powder, salt, baking soda and baking powder. Slowly stir in the wet ingredients, being careful not to overmix. Fold in chocolate chips. The batter will be a little chunky.
  4. Divide the batter between the 12 muffin cups – fill them all the way to the top. Take 1 teaspoon of melted peanut butter and spoon it on top of the batter. Swirl it around with a knife or a toothpick. Sprinkle with peanut butter chips. Repeat with all 12 cupcakes.
  5. Bake for 18-20 minutes or until a toothpick inserted into the middle comes out clean. Allow muffins to cool for 3 minutes, then transfer to a wire rack to cool completely. Muffins stay fresh in an airtight container at room temperature for up to 5 days.


  1. Yogurt: You can use low fat, nonfat, vanilla, or plain Greek yogurt or regular yogurt.
  2. Peanut Butter: Natural peanut butter is OK, do not use powdered peanut butter.
  3. Sift Dry Ingredients: Be sure to sift your dry ingredients together to avoid pockets of cocoa powder lumps. If you have no sifter, whisk the dry ingredients together very well to remove the lumps.

Keywords: healthy chocolate peanut butter swirl cupcakes, healthy cupcakes


Comments are closed.

  1. These are really good! my only problem was they really stuck to the paper liners

  2. Hi Sally! I have attempted baking your death by chocolate cupcakes and it turned out pretty good! It was my very first time as I have never baked before 😀 So, thanks very much for sharing your recipe! 🙂 By the way, I realised that the paper cup base was filled with some tiny oil spots, do you know the cause of that? Please advise!

    For the skinny chocolate peanut butter swirl cupcakes, is it OK if I replace the dark chocolate chips with dark chocolate bar instead? Should I chop them into pieces? Thanks and looking forward to your reply! 🙂

  3. Hi Sally!

    Just wanted to say I just made these and they look amazing, I can’t wait to eat them! I’ve been following your blog for well over a year and baked heaps of your recipes but never left a comment. I just wanted to say I think you’re amazing and I love your recipes – they are the first thing I look at when I’m taking a break from study 😉

    Thanks and keep the deliciousness coming!

    1. Thanks for saying hi, Melissa! I appreciate it. 🙂 Happy you enjoy my recipes!

  4. These look fabulous! I’ve made many of your other recipes, and they have all turned out wonderfully, so I am very eager to make these as well. Thanks for sharing!

    One question, though – can these be frozen, and then just heated up in the microwave whenever we want to eat them? Or will they become very dry?

    1. I freeze them all the time – in fact, I think I have a few in my freezer right now. A quick round in the microwave to reheat/defrost does the trick. They’re still quite tasty.

      1. Perfect; thanks so much! I’m sure I’ll enjoy these immensely!

  5. Hi…the recipe looks delish. . but I hate bananas..What can I use instead?

  6. OMG! Made these today! These little gems are big, dense,just the right amount of sweetness……YUMMY!

    I am thinking of trying to make them into a banana chocolate chip cupcake. I have a friend’s banana bread recipe that is to die for. Thinking about using your base and her spices. One question…..would I use more flour in the place of the cocoa powder? Another banana and 1/4 cup more flour? What do you think?

    Can’t wait to try your other cupcakes. I think I will be the cupcake of the month baker/teacher and take a new one to school every month. Think I’ll be the principal’s pet? LOL

    Thanks! Karen

    1. Hey Karen! You could try using my banana peanut butter muffins recipe (they have chocolate chips) instead:

      Otherwise, I can’t give any recommendations for leaving out the cocoa here. It’s not really an even swap with flour.

      1. I’ll take a look at that recipe. Wasn’t sure about the swap! Thanks for letting me know! I can’t wait to try some of the others. Where to start? They all sound so delicious! 🙂

  7. Hi Sally! I love your blog and your recipes. I had recently tried the homemade dog treats for my puppy and it was great to see him drooling over them. I didn’t have a cookie cutter so I carved the shapes out with a knife with his name. Thank you for sharing it 🙂

    I just gave these wonderful cupcakes a try. I halved the ingredients for 6 cupcakes and did everything else as per the recipe but for some reason they came out underdone after 20 minutes (they were badly stuck to the liners and gooey inside) I did try to keep them a little longer but that didn’t help. Do you know what could have gone wrong? They still taste pretty awesome but I would love to bake them again and get them to look like yours 🙂


  8. Grannie Annie says:

    I substituted no salt peanuts for peanut butter chips and added some choc chips to tops too, great Birthday cupcakes for my son’s BD! Thanks Sallie!

  9. Just made these last night from your cookbook (I took it out of my library for a test run!) and already my family is hooked! Made it in the 8×8 pan and it was so hard to wait until they cooled to eat them. I could have polished the whole thing off myself!!!

    1. Thanks so much Catherine! I love it in cake form.

  10. Hi Sally, I have really been enjoying your site over the past few months and tried a number of your recipes. My coworkers and my husband’s coworkers have been the lucky taste-testers who have gotten to enjoy all the treats. I have a question for you- If I’m not a big fan of bananas, could I substitute apple sauce or more yogurt and what woudl the substitution be? Thanks!

    1. Hi Keara. For these, use 1/2 cup applesauce and 1/2 cup melted coconut oil (or other oil)– this would be the best choice. I fear the cupcakes will taste “gummy” with 1 full cup of applesauce

  11. Hi Sally
    These look incredible – chocolate + pb is always a winner in my book! I love your informative posts and corresponding pics, I find it really brings the recipes alive.

    Any suggestions for what I could use instead of yogurt to make a non-dairy version?
    If not, hubby will just go without….more for me 😉

    1. How about unsweetened applesauce? Thanks for the compliments, I’m so happy you enjoy my blog and recipes Patty.

  12. So I REALLY want and NEED to try these, but is the wheat flour able to be completely replaced by the all purpose flour and if it can is it a different amount of flour that needs to be measured? Thanks 🙂

    1. You can use an equal amount of all-purpose flour instead.

  13. If they taste half as good as the mouthfull of batter and “icing” I just ate, than this is a keeper recipe…. FOR SURE!

  14. Thanks Sally,for all your superb recipes,I find myself reading your blog often,its so engrossing and you really go into such detail.Every recipe I’ve tried so far are simply excellent.A few points though:unable to get one or two ingredients here in I improvise and adapt,but I can’t find peanut butter chips.Such a pity.I’m thinking of suggesting this to Nestle or one of them.Do you have any idea where I could find these little pb chips,I live in West Sussex…near London.Thanks again.Sylvie.

    1. How about online? Not sure what shipping would be like. You can just use chocolate chips instead if that is easier.

  15. I just finished making these delicious little muffins. Wow, my new go to banana muffin recipe! I made them in my mini muffin pan, which made about 36 muffins. Using only two bananas made for a nice subtle banana flavor. I was out of regular baking cocoa and used Hershey’s Special Dark Chocolate cocoa. I worried that the chocolate flavor might be a little too strong, but it was perfect. I added about 1/3 cup of milk chocolate chips and walnuts too. Great recipe! They are so moist, it is hard to believe there isn’t any butter in these. They are so good straight from the oven that I didn’t even think to add the peanut butter on top. I don’t think I will either; they are so good just the way they are! Thank you for the recipe.

  16. I made these tonight. They were a big hit, had to try. Made them for a potluck on Saturday. Instead of normal sized cupcakes I did mini cupcakes. My concern/question is they stuck to the paper liners something horrible. What caused this? How can I prevent it next time? Thanks. This is the first time I’ve come to your blog, and won’t be the last!

    1. Hi Kari– so glad you gave these a try. Are you using little paper wrappers? I always like to use the little wrappers that are foil. I never, ever have problems with sticking using those.

  17. Sally these were soooooo good!!! Thank you!!!

  18. I’m thinking of baking these, and pretty optimistic about what the outcome will be (I mean, chocolate and peanut butter, I just had to) but I was wondering if there is a calorie count on these.

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally