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Healthy chocolate cupcakes displayed on a cake stand.
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5 from 3 votes

Healthy Chocolate Cupcakes

These healthy chocolate cupcakes are made with whole wheat pastry flour and less butter and sugar than traditional cupcakes. They're light, fluffy, easy to make and perfect for any celebration!
Prep Time10 minutes
Cook Time15 minutes
Total Time25 minutes
Course: Dessert
Cuisine: American
Keyword: Healthy Chocolate Cupcakes
Servings: 12


  • ½ cup almond milk
  • 1 teaspoon apple cider vinegar
  • ½ cup cane sugar
  • ¼ cup butter softened, at room temperature
  • 2 large eggs at room temperature
  • ¼ cup applesauce at room temperature
  • 1 teaspoon vanilla extract
  • 1 cup whole wheat pastry flour, white whole wheat flour or all purpose flour
  • cup cocoa powder
  • 1 teaspoon baking powder
  • ½ teaspoon salt
  • Chocolate frosting of choice I used Simple Mills
  • Chocolate sprinkles for topping, optional


  • Preheat oven to 350°F. Line a 12 cup muffin pan with paper or silicone liners.
  • Whisk almond milk and apple cider vinegar in a medium bowl and let curdle for 5-10 minutes. Set aside.
    Apple cider vinegar mixed with almond milk in a measuring cup.
  • Add sugar and butter to a large mixing bowl and whip with a hand mixer on medium speed until fluffy, about 3-5 minutes. Alternatively, you can use a stand mixer.
    Butter and sugar whipped together.
  • Add eggs, applesauce and vanilla extract and whisk until combined on low medium speed.
    The beginning of cupcake batter in a bowl.
  • Slowly add almond milk mixture while mixing on low.
    Almond milk added to cupcake batter.
  • Add flour, cocoa powder, baking powder and salt and whisk on low until just combined and batter is smooth.
    Chocolate cupcake batter.
  • Pour batter evenly between 12 muffin tins. Bake for 14-15 minutes or until a toothpick inserted in the center of the cupcake comes out clean.
    Batter portioned into twelve lined cupcake cavities.
  • Let cupcakes cool in the tin for a few minutes or so, then remove and let cool completely on a wire rack.
    Twelve baked cupcakes.
  • Once cupcakes are completely cool, frost, top with sprinkles if desired and serve.
    Icing a healthy chocolate cupcake with chocolate frosting.



  • Almond milk: Not all non-dairy milk will work for vegan buttermilk, but soy milk and oat milk should work if you don’t have almond milk on hand.
  • Apple cider vinegar: If you don't have apple cider vinegar on hand, white vinegar or lemon juice works just as well.
  • Cane sugar: You can swap cane sugar out for granulated sugar or coconut sugar.  
  • Butter: If you need this recipe to be dairy-free, vegan butter should work as a substitute.
  • Eggs: I haven’t tested an egg-free version of these cupcakes, but let me know if you decide to experiment in the comments below!
  • Applesauce: This helps to replace some of the butter, but if you don't have applesauce on hand, mashed bananas, Greek yogurt or more butter will work just fine.
  • Flour: If you don't have whole wheat pastry flour on hand cake flour or all-purpose flour should work just fine. To make these cupcakes gluten-free just use a gluten-free 1:1 flour like Bob’s Red Mill gluten-free 1:1 all-purpose flour. The cupcakes might turn out a little denser with the gluten-free flour, but it should work just fine.
  • Frosting: I love chocolate frosting on chocolate cupcakes, but feel free to use your favorite flavor of frosting. If you don't want to go the chocolate route you could try my healthy cream cheese frosting or peanut butter greek yogurt frosting instead.


Serving: 1 cupcake w/o frosting | Calories: 128kcal | Carbohydrates: 18g | Protein: 3g | Fat: 5g | Saturated Fat: 3g | Monounsaturated Fat: 1g | Cholesterol: 41mg | Sodium: 188mg | Potassium: 113mg | Fiber: 1g | Sugar: 9g