The Ultimate Healthy Dark Chocolate Cupcakes
Yields: 12 cupcakes
These cupcakes are a chocoholic’s dream! They’re rich, tender, and easy to make. That fudgy dark chocolate frosting really takes them over the top! Leftovers will keep for at least 5 days if stored in an airtight container in the refrigerator.
  1. 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.
  2. 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.)
  3. 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.
  4. 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 vanilla crème stevia. Stir until thoroughly combined. Spread on top of the cooled cupcakes.
Notes: These cupcakes are meant to taste similar to 72% dark chocolate. For sweeter cupcakes, substitute additional pure maple syrup for some or all of the milk. For sweeter frosting, mix in additional vanilla crème stevia to suit your tastes.

Do not substitute Dutched or special dark cocoa powder. They’ll make the cupcakes taste bitter, and the cupcakes already taste really rich and chocolaty without those two varities!

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 blends will work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour, and all-purpose flour may be substituted for the white whole wheat flour.

Honey or agave may be substituted for the pure maple syrup. Alternatively, ⅔ cup (128g) granulated sugar plus an additional ¼ cup (60mL) nonfat milk may be substituted as well.

Any milk may be substituted for the nonfat milk.

If you prefer not to use the vanilla crème stevia in the frosting, substitute 3 tablespoons (45mL) of pure maple syrup, honey, or agave and decrease the nonfat milk to 5 tablespoons (75mL). You may also adjust the amount of pure maple syrup, honey, or agave to suit your tastes.

It’s VERY important to measure the cocoa powder correctly, like this. Too much cocoa powder in either the cupcakes or the frosting will make them taste dry and bitter, instead of rich and dark chocolaty.

{gluten-free, clean eating, low fat, low calorie}
Recipe by Amy's Healthy Baking at