The Ultimate Healthy Dark Chocolate Cupcakes | Amy's Healthy Baking (2024)

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An easy recipe for rich dark chocolate cupcakes topped with fudgy dark chocolate frosting. They taste sinfully decadent, so it’ll be our little secret that they’re actually healthy & lower calorie!

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!

Click here to PIN the recipe and save it for later!

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

IMPORTANT MEASURING NOTE – READ BEFORE BEGINNING: It's very important to measure the flour and cocoa powder correctly, using this method or a kitchen scale. (← That’s the one I own and love!) Too much flour and cocoa powder in the batter will make your cupcakes dry and crumbly, instead of soft, moist, and fudgy. Too much cocoa powder will also make your cupcakes taste bitter, instead of rich and dark chocolaty.

IMPORTANT FLAVOR NOTE – READ BEFORE BEGINNING: These cupcakes are meant to taste similar to 72% dark chocolate. If you'd prefer sweeter cupcakes, substitute additional pure maple syrup for some or all of the milk. (For example, use ⅔ cup + 2 tablespoons {190mL} of pure maple syrup and 2 tablespoons {30mL} of milk instead.)

For sweeter frosting, see the "Stevia Notes + Alternatives" section below.

COCOA POWDER NOTES: If your cocoa powder is very bumpy and/or clumpy, then sift it into the mixing bowl.

I do not recommend substituting Dutched or special dark cocoa powder. Both of these have a different acidity level, which will affect the taste and texture of your cupcakes. I've also found they have a blander and noticeably muted chocolate flavor when used to make these cupcakes. For the best results, use regular unsweetened cocoa powder.

FLOUR ALTERNATIVES: Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.

PURE MAPLE SYRUP NOTES + ALTERNATIVES: Honey or agave may be substituted for the pure maple syrup. Alternatively, ⅔ cup (128g) of coconut sugar or granulated sugar PLUS an additional ¼ cup (60mL) nonfat milk may be substituted for the pure maple syrup instead.

Do not substitute sugar free maple syrup in the cupcake batter! If you do, your cupcakes will collapse some while cooling and turn out overly dense.

MILK ALTERNATIVES: Any milk may be substituted for the nonfat milk in the batter and frosting.

STEVIA NOTES + ALTERNATIVES: Some people are more sensitive to the taste of stevia when it's used "raw," like in this frosting (as opposed to when used in batters or doughs that are baked in the oven). If that's you, then I highly recommend using one of the sweetener alternatives below to make this chocolate frosting instead!

Many stevia brands and products have different sweetness levels, so they’re not always 1-for-1 substitutes for each other. For the best results, use the same liquid stevia that I do. I buy it online here (← that’s the best price I’ve found!), and you’ll use it in all of these recipes of mine too!

If you prefer not to use the liquid stevia in the frosting, substitute 3 tablespoons (45mL) of pure maple syrup, honey, or agave and decrease the nonfat milk to 5 tablespoons (75mL). Although it won't work in the cupcake batter, sugar free maple syrup will work in the frosting, if you'd prefer a different no-calorie sweetener option.

For sweeter frosting, use additional liquid stevia (if that's your sweetener of choice!). Alternatively, if using the option of milk + maple syrup, honey, or agave, then substitute additional sweetener for an equal amount of milk. (For example, use 5 tablespoons {75mL} of maple syrup and 3 tablespoons {45mL} of milk.)

GLUTEN FREE OPTION: For the gluten free flour, I recommend as follows: ½ cup (60g) millet flour, 2 tablespoons (30g) tapioca flour, 2 tablespoons (30g) brown rice flour, and ½ teaspoon xanthan gum. Many store-bought gluten free flour baking blends (I like this one from Bob's Red Mill) will work as well, if measured like this.

HOW TO STORE: Leftover cupcakes should keep for at least five days if stored in an airtight container in the refrigerator.

{gluten free, clean eating, low fat, low calorie}

DID YOU MAKE THIS RECIPE?I'd love to hear what you think of it in a comment below! If you take a picture, tag @amys.healthy.baking on Instagram or use the hashtag #amyshealthybaking.

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!