Healthy Chocolate Cupcakes with Chocolate Ganache

Healthier dark chocolate cupcakes made using almond flour and sweetened with coconut sugar for tender and moist crumb. This easy cupcake recipe is made gluten free, dairy free, refined sugar free and keto friendly so everyone can enjoy!

Easy Cupcake Recipe with chocolate ganache and strawberry hearts

Chocolate cupcakes topped with chocolate ganache and fresh strawberries? Is there a better way to celebrate Valentine’s Day?

I took one of my favorite almond flour cake recipes and used it as a base recipe for these cute little gluten free cupcakes.


Easy cupcake recipe with chocolate ganache and strawberries
gluten free cupcakes in a pink tin with chocolate ganache and strawberries

How to make cupcakes

This easy cupcake recipe is made using simple and wholesome ingredients and comes together so quickly, you will never buy boxed cake again.

Here’s what you need:

  • almond flour – I used a finely ground almond flour. You could also use a hazelnut flour but you cannot substitute any other flour in this recipe.
  • unsweetened cocoa powder & unsweetened special dark cocoa powder – you can use all regular cocoa powder if you can’t find special dark. Keep in mind the color will not the same.
  • baking soda – this acts as a leavening agent to help the cookies rise
  • salt – salt enhances the flavors of the cookie
  • organic eggs
  • applesauce – the original recipe I made called for 6 eggs so when I updated the recipe, I subbed applesauce for two of them to make it a more approachable recipe. If you don’t have applesauce on hand, use 2 eggs in its place.
  • coconut oil – the oil will keep the chocolate a tad softer once it hardens.
  • vanilla extract
  • coconut sugar – you can use any granulated sweetener you like as well as erythritol for keto
  • almond milk – or any nut milk
  • coconut milk – full fat from the can is the only coconut milk that will work here
  • dark chocolate chips – or you can used semi sweet chocolate chips or chopped chocolate. I love Hu Kitchen and Lily’s brands
  • strawberries – optional

Chocolate Cupcakes with Almond Flour

Do cakes with almond flour rise?

This easy cupcake recipe calls for baking soda as a leavening agent which helps the cake rise and creates a tender crumb.

Does almond flour make a cake moist?

Almond flour is high in fat which helps to ensure your cake is moist and tender. 

Can almond flour replace all purpose flour?

I found that you cannot replace almond flour with all purpose flour with having to adjust other ingredients such as eggs or other liquids.

low carb Valentine's Day treats in a pink pan with strawberries and chocolate ganache


Here are a few of my favorite chocolate cake recipes on my blog. I know you will love them as much as I do!

Gluten Free Chocolate Cupcakes

Double Chocolate Hazelnut Cupcakes

Dark Chocolate Peanut Butter Cupcakes

Easy Chocolate Cupcake Recipe

Decadent chocolate almond flour cupcakes topped with rich two ingredient chocolate ganache frosting and strawberry hearts.
Pin Recipe
Prep Time30 minutes
Cook Time28 minutes
Total Time58 minutes
Course: Dessert
Cuisine: American
Keyword: almond flour, cake, chocolate, chocolate cupcakes
Servings: 16 cupcakes
Calories: 264kcal
Author: Ciarra Siller


  • Mixing bowls
  • Cupcake Pans


  • 3 cups almond flour finely ground
  • ½ cup unsweetened cocoa powder
  • ½ cup unsweetened special dark cocoa powder
  • 2 tsp baking soda
  • ½ tsp salt
  • 4 organic eggs room temperature
  • cup applesauce unsweetened
  • ¼ cup coconut oil melted
  • 2 tsp vanilla extract
  • 1 cup coconut sugar or granulated sweetener of choice erythritol for keto
  • 1 cup almond milk room temperature

for the frosting

  • 4 oz dark chocolate chips or chopped chocolate refined sugar free
  • ½ cup full fat coconut milk
  • 1 cup strawberries


for the cupcakes

  • Preheat oven to 350 F and prepare a cupcake pan with liners.
  • Sift together the almond flour, cocoa powders, baking soda and salt in a large bowl and stir until combined. In another bowl, whisk together the eggs, apple sauce, coconut oil, vanilla and coconut sugar until smooth and fluffy. Add the wet ingredients to the dry and whisk until to combine while adding the almond milk. Distribute the batter between the liners, filling them about ¾ full. Bake cupcakes for 23-26 minutes or until cooked through. 

for the ganache

  • Once the cupcakes have cooled, place the chocolate into a heat proof bowl.
  • Add the coconut milk to a small sauce pan and heat until simmering. Pour the hot milk over the chocolate and let it sit for 5 minutes before stirring smooth. Let the ganache sit for 5 minutes to cool slightly.

assemble cupcakes

  • Dip the top of each cooled cupcake into the chocolate ganache. Place them in the refrigerator for 5 minutes for chocolate to harden, dip again for a second layer and then top with strawberries and sprinkles if desired. Chill until chocolate is solid, about 5 minutes.


These cupcakes are best if served immediately or stored in an airtight container in the refrigerator for up to 3 days.








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Albert Bevia - Spain on a Fork
Albert Bevia - Spain on a Fork
6 years ago

These cupcakes look so good! love that blood orange frosting, now that is taking seasonal food to the next level…amazing

Almond Strawberry Coffee Cake | Peanut Butter Plus Chocolate
3 years ago

[…] Chocolate Cupcakes with Blood Orange Frosting […]

1 year ago

What can I replace the applesauce with? Can’t eat apples at all. I have a bunch of leftover buttercreams in my refrigerator. These would perfect for using them up. Thank you!

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I'm Ciarra

Welcome to Peanut Butter Plus Chocolate, where I share indulgent dessert recipes. Here you can find healthier versions of your favorite desserts.



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