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!

After sharing my healthy vanilla cupcakes last year I knew I needed to develop a healthy chocolate cupcake recipe for all my chocolate lovers out there!

Just like with my vanilla cupcakes these ones are made healthier with whole wheat pastry flour instead of white flour and less sugar a butter than traditional chocolate cupcakes. But don’t worry, they’re still fluffy and loaded with lots of chocolatey goodness!

Why You’ll Love These Cupcakes

• The chocolate cupcakes topped with chocolate frosting is chef’s kiss!
• Made with whole wheat flour and have less sugar and butter than classic chocolate cupcakes!
• Can easily be made in advance for an upcoming celebration.

Ingredients Needed

• almond milk – most classic cupcake recipes call for buttermilk or sour cream, so we’re making our own dairy-free “buttermilk” by mixing apple cider vinegar with almond milk (store-bought or homemade almond milk works)! Whisk the ACV and almond milk and set aside at room temperature. The mixture should bubble, thicken and potentially even curdle after a few minutes.
• apple cider vinegar – when shopping for ACV, look for a brand that’s unpasteurized with “the mother” included. This is where all the nutrients are. I personally recommend Bragg’s apple cider vinegar. It’s organic, raw and the best of the best.
• cane sugar – cane sugar is less processed than granulated sugar, but white sugar will also work in this recipe.
• butter – we’re creaming the butter and sugar together with a hand mixer, which helps achieve a fluffy cupcake!
• eggs – make sure your eggs are at room temperature before mixing them with the wet ingredients. I won’t get into the science behind it but it’s key for fluffy cupcakes!
• applesauce – to replace some of the butter, we’re using applesauce to help keep these cupcakes moist and fluffy. You’ll want to make sure your applesauce is also at room temperature.
• vanilla extract – a flavor enhancer!
• whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy texture that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour. All-purpose flour or cake flour should work as a substitute.
• cocoa powder – you can’t have chocolate cupcakes without cocoa powder! Make sure you’re using unsweetened cocoa powder. Cacao powder works as well. I love using Navitas organic cacao powder.
• baking powder – to help the cupcakes rise.
• salt – to bring the flavors together.
• chocolate frosting – feel free to use your favorite homemade or store-bought frosting! I used Simple Mills chocolate frosting, but my healthy chocolate frosting would also be delicious.
• chocolate sprinkles – optional, but they definitely make these cupcakes more festive!

How to Make

Whisk almond milk and apple cider vinegar in a medium bowl and let curdle for 5-10 minutes. Set aside.

Add sugar and butter to a large bowl and whip with a hand mixer on medium speed until fluffy, about 3-5 minutes. Alternatively, you can use a stand mixer. Add eggs, applesauce and vanilla extract and whisk until combined on low-medium speed. Slowly add almond milk mixture while mixing on low.

Add dry ingredients (flour, cocoa powder, baking powder and salt) and whisk on low until just combined and batter is smooth.

Pour batter evenly between 12 muffin tins lined with cupcakes liners. Bake for 14-15 minutes at 350°F or until a toothpick inserted in the center of the cupcake comes out clean.

Let cupcakes cool in the tin for a few minutes or so, then remove and let cool completely on a wire rack. Once cupcakes are completely cool, frost, top with sprinkles if desired and serve.

Substitutions & Notes

• 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: This ingredient helps to make the dairy-free “buttermilk,” but 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. I haven’t tried using a liquid sweetener like maple syrup or honey so I’m not sure how these cupcakes would turn out, but let me know if you try it in the comments below!
• 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.

Tips For Success

• Make sure your ingredients are at room temperature – For the best results, make sure your eggs, butter and applesauce are at room temperature! If your ingredients are super cold it could change the structure or texture of your cupcakes.
• Cream your butter and sugar for 3-5 minutes – Make sure you’re beating the butter and sugar together with your hand mixer for 3-5 minutes for the best results. This will help result in fluffy, light cupcakes!
• Transfer cupcakes to a wire rack to cool completely – Let the chocolate cupcakes cool for just a few minutes in the muffin tin and then remove to let cool completely on a wire rack. Don’t leave the cupcakes in the tin for too long because they’ll continue to bake and could dry out!
• Don’t over bake – To ensure you don’t over bake these cupcakes, set your timer for the low end of the suggested bake time.
• Use muffin liners – I highly recommend using silicone muffin liners or parchment baking cups for the best results and to avoid the cupcakes from sticking too much. I also recommend spraying your liners with a little cooking spray. Make sure to let your cupcakes cool completely before trying to remove the liners otherwise they could stick.
• Use a piping bag to frost cupcakes – For the best results scoop your frosting into a piping bag or a plastic baggie. Cut the corner of the baggie and pipe out the frosting on your cupcakes.

How to Make in Advance

These healthy chocolate cupcakes can be made 1-2 days in advance. To make ahead of time, let the cupcakes cool completely and store them in the fridge, covered until you’re ready to frost and serve. Alternatively, you can frost and decorate the cupcakes and store them covered in the fridge until ready to serve!

How to Store Healthy Chocolate Cupcakes

Store any leftover cupcakes in an airtight container on the counter for 1-2 days or in the fridge for up to 5 days. For longer storage, you can store these cupcakes in the freezer for up to 3 months. If you’re storing these in the freezer I would recommend storing them unfrosted. The day before you’re ready to serve, let them thaw in the fridge then frost and decorate as desired!

More Healthy Desserts to Try

Be sure to check out all of the popular dessert recipes here on EBF!