While writing my Healthier Chocolate Treats cookbook, I debated which recipe to feature on the front cover for a very long time. Should it be something classic, like the chocolate chip cookies on P.76 or the fudgy brownies on P.84? Something that looked over-the-top decadent, like the peanut butter cup cheesecake on P.122? An assortment of baked treats?
Eventually, I settled on the dark chocolate cupcakes (P.114), one of my favorite desserts in the entire cookbook. When I awoke on the day of the cover photo shoot, I felt a few butterflies flitting about my stomach as the morning sped past. Even though we’re not supposed to, people still judge a book by its cover… I thought. So it has to be perfect! No pressure or anything, Amy… Oof!
In the kitchen, I sifted through my collection of 31 different paper liners, trying to find the ideal pattern and shade, preferably something that looked subtle and classy. From the back of the drawer, I picked out a sleeve of simple black liners, knowing those would let the tall frosting swirls and plum-colored title text shine.
After pulling the cupcakes from the oven and smelling their tantalizing rich cocoa aroma for what felt like years as they cooled on the counter, I filled a piping bag with the sweet light brown frosting, sneaking a taste from the spatula, and bent over the first treat, which sent the butterflies into a frenzy, threatening to burst out of my chest. Breathe, it’s okay; no pressure! I reminded myself.
I surveyed my tall frosting swirls, selected the three that looked the best, and carefully carried those cupcakes over to the table. After scattering a few baby pink and pastel purple sprinkles around the table, I turned on my camera, peered through the viewfinder, and pressed my finger down on the shutter before checking the image on the tiny digital display. Then repeated. Again and again and again, until I finally captured the perfect shot.
Whew!
When Healthier Chocolate Treats came out as both a hardback cookbook and an eBook (EEK I was so excited!! You can see a special sneak peek and preview what’s inside here and order a copy too!), I thought the best way to celebrate would be with these Ultimate Healthy Dark Chocolate Cupcakes! They’re slightly different than those in my cookbook, topped with my all-time favorite fudgy chocolate frosting instead, and taste as rich and decadent as the ones you’d buy from a bakery.
So it’ll be our little secret that they’re incredibly easy to make and completely healthy!
The recipe begins with two key ingredients: white whole wheat flour and unsweetened cocoa powder. White whole wheat flour is made by finely grinding a special type of white wheat, whereas regular whole wheat flour comes from a heartier variety of red wheat. This gives white whole wheat flour a lighter taste and texture, similar to that of all-purpose flour, but it still has the same health benefits as regular whole wheat flour.
Note: Whole wheat pastry flour would be the perfect substitute, and I’ve included my preferred gluten-free flour blend in the Notes section, too.
As for the second part, you just need regular ol’ unsweetened cocoa powder! Because you’ll use 1 full cup, the cupcakes already taste really rich and dark chocolaty without Dutched or special dark cocoa powder. I actually recommend not substituting either of these. They have a different acidity level, which will affect the taste and texture of your cupcakes.
It’s also incredibly important to measure the cocoa powder correctly, using either a light hand with the this method or a kitchen scale. I highly recommend the latter! This is the inexpensive one that I own, and it was the best $20 I’ve ever spent. I use it every day! Too much cocoa powder will dry out your cupcakes and make them taste bitter, but my trusty kitchen scale ensures that these cupcakes turn out perfectly tender and rich every time.
To keep the cupcakes clean eating friendly, you’ll sweeten them with pure maple syrup instead of refined sugar. Be sure to use the real kind! Avoid pancake syrups or sugar-free syrups; those contain other ingredients that will affect the texture of your cupcakes. Pure maple syrup typically comes in thin glass containers or squat plastic jugs, and the only ingredient on the label should be “maple syrup.” You can typically find it near the other sweeteners at the grocery store, as well as online!
Low-fat cupcakes tend to stick to liners like superglue, so I have a special trick to get around that… Coat the cupcake liners with nonstick cooking spray! This simple tip means the liners will peel away much easier from the cupcakes once they’ve completely cooled. And if the cupcakes still stick more than they should, seal them inside of an airtight container for at least 24 hours to help loosen the liners a little more.
And now for my favorite chocolate frosting! It’s really rich and fudgy, almost like spreading fudge on top of the cupcakes… Pure bliss! Even better, it’s mindlessly easy to make! Simply stir together unsweetened cocoa powder, milk, vanilla, and a little liquid stevia in a bowl. That’s it! You just need a fork — no mixer required — which makes clean-up a breeze!
Note: Stevia is a plant-based, no-calorie sweetener that’s clean eating friendly, and a little goes a long way. You’ll only need ½ teaspoon! This is the kind that I buy because I love its sweet flavor and don’t notice a strange aftertaste, like with some other stevia products. You can find it at many health-oriented grocery stores, but I generally buy it online because that’s the best price I’ve found. (And you’ll use it in all of these recipes of mine, too!)
Time to celebrate the Healthier Chocolate Treats cookbook! (And maybe with a second cupcake too… Or even a third!)
When you bake yours, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! 🙂 ) I’d love to see your healthy chocolate cupcakes!

The Ultimate Healthy Dark Chocolate Cupcakes
Ingredients
FOR THE CUPCAKES
- 1 cup (80g) unsweetened cocoa powder (measured like this)
- ¾ cup (90g) white whole wheat flour or gluten free* flour (measured like this)
- 2 tsp baking powder
- ¼ tsp salt
- 2 tbsp (28g) unsalted butter or coconut oil, melted and cooled slightly
- 2 large eggs, room temperature
- 1 tbsp (15mL) vanilla extract
- ¼ cup (60g) plain nonfat Greek yogurt
- ⅔ cup (160mL) pure maple syrup
- ¼ cup (60mL) nonfat milk
FOR THE FROSTING
- ¾ cup (60g) unsweetened cocoa powder (measured like this)
- ½ cup (120mL) nonfat milk
- 1 ½ tsp vanilla extract
- ½ tsp liquid stevia (see Notes!)
Instructions
- To prepare the cupcakes, preheat the oven to 350°F. Line 12 muffin cups with paper liners, and generously coat the liners with cooking spray.
- In a medium bowl, whisk together the cocoa powder, flour, baking powder, and salt. In a separate bowl, stir together the butter or coconut oil, eggs, and vanilla. Mix in the Greek yogurt, stirring until no large lumps remain. Stir in the pure maple syrup. Alternate between adding the flour mixture and the milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
- Divide the batter between the prepared paper liners. Bake at 350°F for 20-22 minutes or until the centers feel firm to the touch and a toothpick inserted into the center comes out clean. Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
- To prepare the frosting, add the cocoa powder to a small bowl, and make a well in the center. Pour in the milk, vanilla, and liquid stevia. Stir until thoroughly combined. Spread on top of the cooled cupcakes.
Notes
View Nutrition Information + Weight Watchers Points
You may also like Amy’s other recipes…
♡ Mint Chocolate Cupcakes
♡ Mini Chocolate Cupcakes (Vegan)
♡ The Ultimate Healthy Red Velvet Cupcakes
♡ Mini Dark Chocolate Raspberry Cupcakes
♡ Funfetti Cupcakes
♡ Mini Dark Chocolate Banana Cupcakes
♡ Pumpkin Cupcakes
♡ Almond Joy Cupcakes
♡ …and the rest of Amy’s healthy cupcake recipes!















Hey there! I just used ur recipe! I was so excited for the outcome. I only wanted to make 6 cupcakes and your recipe said 12, so I halved everything exactly. I didn’t make the frosting. However, when I tried the cupcakes, they were quite dry and not sweet. What do you recommend? Thank you.
I really appreciate your interest in my recipe Alicia! We’ll get this sorted out so your cupcakes turn out perfectly rich and tender. 🙂 How did you measure the cocoa powder? Did you scoop it directly from the container with your measuring cups/spoons?
Amy, these cupcakes are DELICIOUS! I am blown away! I’m pregnant and have had a strong craving for cake for several weeks, so I decided to finally give in with a healthy treat. I have tried many baked goods with white whole wheat, Greek yogurt, little butter, etc., and they’ve been barely edible (honestly, quite terrible) – but your recipe knocked it out of the park! I baked it in one 9-inch springform pan for the same amount of time and was easily able to slice it horizontally in half and ice the middle; the cake held together and didn’t fall apart. My husband – I wish I could describe just how picky he can be – took a bit and said, “Mmh, that’s pretty good.” When I need an alternative to full-fat and high-sugar desserts, this is now my go-to. Now my only problem is trying to not eat too much in one sitting. ; ) Thank you for sharing!
Oh my goodness!! That’s such high praise from both you and your husband — I’m truly honored!! Thank you for sharing that with me! 🙂 I’m so glad you loved this recipe, and it means so much to me that you’d call it your new go-to!!
HI Amy!
Do you know the breakdown of the carb amount between the icing and the cupcake?
I’m going to make these with a different (white) icing recipe for my daughter’s birthday. Her older sis has type 1 diabetes so we need to give her insulin for the carbs and I’m just wondering how much of the 25.9g of carbs here is the cupcake vs. the icing. Thank you!
I really appreciate your interest in my recipe Kate! I’m truly honored that you’d like to make these for your daughter’s birthday. That means a lot to me! 🙂 If you make the recipe exactly as written, there should only be about 0.5-1g of carbs in the frosting. This is the free nutrition calculator that I use, if you’d like to know the precise carb breakdown! I can’t wait to hear what everyone thinks of the cupcakes — and happy birthday to your younger daughter!
These are so chocolatey and delicious! The consistency was great right out of the oven but they were a nit dry by the next day. Great, more healthy chocolate cupcake recipe.
I’m so glad you enjoyed these cupcakes Cassie! 🙂 How did you store your cupcakes? And how did you measure the cocoa powder — with measuring cups or a kitchen scale?
These are good, but definitely less cocoa as it was a little strong for me.
I’m glad you enjoyed these cupcakes Gustav! 🙂 How did you measure the cocoa powder? Did you use measuring cups or a kitchen scale?
Thanks for the recipe Amy!, made them today for a meeting tomorrow, was looking for something with natural sugars for a diabetic lady who will be at the meeting. They have come out perfect. I doubled the frosting and did swirls. Wish I could shoe you a picture on here.
Off to Galavant through your other recipes now X
I’m SO glad you enjoyed these cupcakes Natalie! I’m truly honored that you made them for a meeting — what a huge compliment! 🙂 You’re welcome to email me a picture of your cupcakes. I’d love to see them! And I can’t wait to hear what you try next!
Cannot find your email address ?
Just click on the “email me” link in my previous comment! 😉
I prepared the healthy dark chocolate cupcakes and they’re dry. Now, I followed the recipe and opted to use the coconut oil. Curious would unsalted butter been a better choice. It’s a gorgeous recipe and I will prepare this recipe again, but can you offer any suggestions in order to have delectable cupcakes.
I really appreciate your interest in my recipe Daniel! Did you watch my video? Is your cupcake batter the same consistency as mine before baking, or does it seem dry then? Also, how did you measure the cocoa powder and flour — with measuring cups or a kitchen scale? Your answer (and as much detail as you can provide!) will really help us solve that dryness issue. 🙂
I’m allergic to dark chocolate. Can go with a milk chocolate. I’d be afraid to try to tweak this recipe on my own! Any Suggestions?
I really appreciate your interest in my recipe Robin! Are you allergic to cocoa powder? That’s the only source of chocolate in this recipe! 🙂
I made these today and for some reason my frosting doesn’t look anything like yours. It is thin and runny. What did I do wrong? I measured correct and used maple syrup instead of vanilla creme because I couldn’t find it. I did use 5 tbsp of milk and 3 tbsp of syrup as your note said. I just don’t understand why it’s so dark and runny. I measured the cocoa powder properly also.
I really appreciate your interest in my recipe Katie! Did you use pure maple syrup, rather than pancake syrup or sugar-free syrup? Were you really careful with measuring the maple syrup and milk? Even a touch too much — like an extra ½ teaspoon — can make a big difference! To make the frosting thicker, you can add more cocoa powder a teaspoon or so at a time. 🙂
Hi Amy
Sorry if asked before but do you have a bake time for mini cupcakes? Making them for my sons class party so need a mini version. Thanks!
15 min did the trick!
I really appreciate your interest in my recipe Lauren! I’m so glad the mini cupcakes turned out. Thanks for letting me know that 15 minutes was the magic number! I can’t wait to hear what your son and his classmates think of these cupcakes! 🙂