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!















See I know these are perfect for me because I’m a HUGE fan of anything dark chocolate, but if I made these for other people I would probably have to sweeten it a little more. So more for me then! 😉 Absolutely gorgeous photos Amy, they look so mouth-watering!!! 🙂
That’s exactly why we’re friends Marina… Both we and our friends have same tastes buds, and we don’t mind extra cupcakes at all! 😉 Thanks for your sweet words about my photos too — that means a lot to me! ♥
I haven’t tried this recipe yet, but is it possible to substitute canned pumpkin puree for egg and oil? I use a recipe for muffins that only require a box of cake mix and a can of pumpkin puree…of course I add chocolate chips. I realize this is not as healthy as your recipe, but maybe the pumpkin as used is something you had not heard or thought about. The muffins are so good(use Duncan Hines Devil’s Food and really good chips)! Makes huge muffins at 18, so for work I usually make stretch to 24). Original recipe said without chips and 18 count muffins they were less than 100 calories. I also make carrot cake muffins with grated carrot added(sometimes cinnamon chips) and spice cake muffins with pumpkin spice chips. Don’t need a lot of chips(hahaha), even 5-6 in each muffin is yummy. I have never made a cake from scratch, but I want to try this summer with your tips plus pumpkin. Thanks for all your hard work, Janet B.
I wouldn’t recommend substituting pumpkin purée in this recipe. The cupcakes will turn out somewhat gummy, as opposed to tender. They’re already much lighter in fat and calories than the cupcakes you’d make from a box mix, so it isn’t necessary to reduce that even further with the pumpkin purée! 🙂 I can’t wait to hear what you think of the recipe if you try it, Janet! (And I can never say no to extra chocolate, especially something as irresistible as melty chocolate chips! 😉 )
Is there a way to make this frosting but vanilla flavored? 🙂
Unfortunately, there isn’t an easy way, but I’m sure vanilla frosting would taste lovely on these cupcakes too! 🙂 I’m excited to hear what you think of them Diana!
Hi Amy,
I’m planning on baking these for my son’s birthday. I need to bake gluten free. What do you think of of Bob’s Redmill Gluten free 1 to 1 baking flour to replace all the ingredients of you gluten free option?
Your son is so lucky to have you to bake him homemade birthday treats Lauren! 🙂 Bob’s Red Mill gluten-free 1-to-1 baking flour should work great. Be extremely careful when measuring it, and don’t taste the raw batter. Bob’s Red Mill includes garbanzo bean flour in that flour blend, which you can’t taste in the cupcakes after they’ve been baked but you can taste in the raw batter. (Trust me, I’ve only made that mistake once! 😉 ) I can’t wait to hear what you and your son think of the cupcakes!
Looks great!
Amy, what is your opinion on flax egg as an egg substitute in baked goods? (If you have any experience on this)
I actually prefer Ener-G as an egg substitute! It’s a shelf-stable powder that keep for ages, and it works in basically all of my recipes, including these cupcakes. For this recipe, use 1 tablespoon of Ener-G whisked with 4 tablespoons of warm water, and add 1 additional tablespoon of either coconut oil or butter. 🙂 I’d love to hear what you think if you try the cupcakes Evan!
Great recipe thank you. Perfect for those Chocolate days 🙂
Last minute I found I didn’t have cocoa and I used carob I know not the same but the came out perfect
Thank you for sharing
I’m so glad that you enjoyed the cupcakes and the carob worked Dvorah! 🙂
Saw these on foodgawker and I just had to comment! These photos are making my mouth water Amy! Seriously incredible! I’ve always loved your site (before I started my own blog) and appreciate your healthy baking swaps! I’ve never tried a chocolate frosting like that with just the powder, milk and stevia, I’ll definitely have to give that a shot. Thank you for sharing, and again seriously love these photos 🙂
You’re so sweet — thank you so much for taking the time to comment Ashley! I always love seeing your comments on Instagram too. 🙂 I can’t wait to hear what you think of the frosting!
i am definitely going to be saving this recipe for some sort of cookout or birthday this summer! these sounds so decadent and look amazing! I wish I could just grab one through the screen 😀
I wish you could too Mia — that would be amazing! 🙂 I can’t wait to hear what you think of the cupcakes when you bake them this summer!
Can you you use milk chocolate to substitute the dark chocolate.
I’m not entirely sure what you mean, Noah. All of the chocolate flavor comes from cocoa powder in these cupcakes! 🙂
Oh never mind thanks.
You’re welcome Noah! 🙂 I’d love to hear what you think of the cupcakes if you try them!
Looks great Amy! I’m a chocaholic and I feel like these would really hit the spot. I have got to get on this vanilla creme stevia thing though. Gonna try to find some at the store today/later this weekend or order from amazon if i can’t! I love your recipes!
I was reading your article about the differences in baking soda vs baking powder because I’m trying to be my own recipe developer. It’s a lot of fun but HARD and that article was really helpful. I actually went home yesterday after work and made some amazing cookies without even modifying a recipe. I was stoked! Have you ever considered writing a Baking 101 book or something like that? You’re so knowledgeable and you could also write one geared towards how to replace ingredients with healthier alternatives! I’d totally buy it!
You’re so sweet Ashley — thank you for your amazing comment! It totally made my day! 🙂 I’ve actually found that the price of the vanilla creme stevia is cheaper if you buy it on Amazon through the link I included when compared to what most grocery stores sell it for. It’s especially helpful if you have Amazon prime too — it’ll come it just 2 days!
And that’s amazing about your cookies from yesterday! Congratulations — how exciting!! 🙂 I absolutely love your idea for a Baking 101 book! I hadn’t considered it before but… I definitely will now!
Hi! These cupcakes really look delicious, I just can’t wait to try them… I have a question, is it possible to use honey instead of maple syrup or would it ruin the recipe? Thanks a lot 🙂
I actually answered that question already in the Notes section underneath the Instructions. 🙂 I can’t wait to hear what you think of the cupcakes Margherita!
Oh right, sorry I didn’t see that at all! Thank you…. I’m definitely gonna try them today, I’ll let you know what I think about them 🙂
It’s easy to miss! 🙂 I’m so excited to hear how the cupcakes turned out!
I tried them yesterday and they were amazing! I just had to add a bit more milk to make the frosting creamy but everything else was perfect. My family lived them, I’m definitely gonna do them again. Thanks for sharing the recipe!
I’m so glad you and your family enjoyed the cupcakes Margherita! That means a lot to me that you’d like to make them again. Thank you for sharing that with me! 🙂