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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 1x
  • 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

Reader Questions and Reviews

  1. I love this recipe! Would there be a way to make it as a cake instead of the cupcakes? Looking for a birthday recipe!

    1. Hi Margaret! I have ever tried it before, but I can’t see why it wouldn’t work in a 8×8 or 9×9 square baking pan. I am unsure of the baking time since I’ve never tried it myself.

  2. I just made these and they are absolutely delicious… The slight undertone of banana combined with rich chocolate and peanut butter – what an amazing combination! And of top of that, it’s healthy (for the most part!).

    I love how the peanut butter is just swirled on top so the flavor doesn’t get lost in the cupcakes. Thanks so much for the fab recipe!

  3. Just made these for the first time and they are delicious! Peanut butter and chocolate make the world a better place. 🙂

  4. 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!!!

  5. 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.

  6. Hi Sally,
    I love your recipes and everything I made from your site turns out perfect on the first try! However these cupcakes turned out almost rubbery in texture. The taste is good, but the texture is pretty unpleasant. Any idea what might have caused that?

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