Paleo Dark Chocolate Cupcakes

Everyone needs an amazing chocolate cupcakes recipe, and this one is ours! These Gluten Free Chocolate Cupcakes are moist with a deep chocolate flavor and simply delicious. They’re also dairy-free and made without any refined sweeteners. Grab a bowl and a whisk and head straight to the kitchen to whip some up!

A close up of a gluten free chocolate cupcake with piped frosting on top.Gluten Free Chocolate Cupcakes

In my opinion, a chocolate cupcake should be at least three things: moist, rich and heavy on the chocolate flavor. These gluten free Chocolate Cupcakes check all those boxes and more! These simple-to-make cupcakes are a bit on the healthier side because they are dairy-free, made primarily with almond flour (hello nutrients!) and contain no added refined sugars. And the bonus is you only need two bowls and a whisk to make them! We have a few different options to frost them, including this dairy-free chocolate frosting. Whip them up for your next celebration or your next I-need-a-chocolate-cupcake kind of night!

Batter being mixed together.

Ingredients Needed

  • Almond Flour
  • Cocoa Powder
  • Coconut flour
  • Baking Powder and Soda
  • Pinch Sea Salt
  • Espresso Powder (optional)
  • Eggs
  • Coconut sugar
  • Milk (We use almond)
  • Avocado Oil
  • Vanilla extract

Frosting Options

We’ve made a few different frosting options over the years. This recipe uses a traditional chocolate buttercream, though it does use butter so it isn’t dairy-free. This recipe is for a vanilla buttercream.

If you need a dairy-free and paleo-friendly version, check out this recipe! It is a whipped chocolate ganache frosting that is simple to make. It’s also the version shown here in the photographs.

Paleo chocolate cupcake with a big bite taken out of it.

If you like this sweet treat, check out these others:

Chocolate Cupcakes with Chocolate Buttercream and Heart Toppers
Yields 9
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Prep Time
10 min
Cook Time
30 min
Total Time
40 min
Prep Time
10 min
Cook Time
30 min
Total Time
40 min
  1. 1 cup blanched almond flour
  2. 1 tbsp coconut flour
  3. 3 tbsp cocoa powder
  4. 1/3 cup chcocolate chunks
  5. 1/4 tsp baking soda
  6. 1/2 tsp baking powder
  1. 3 eggs
  2. 3 tbsp apple sauce
  3. 3 tbsp raw honey
  4. 1 tsp vanilla
  1. 1 cup grass-fed butter, softened
  2. 1 cup dark chocolate chunks, I use Enjoy Life's, Guittards, or Whole Foods brand
  3. 2 tbsp full-fat coconut milk, more as needed
  4. 1/4 cup cocoa powder
  5. 1 cup organic powdered sugar
  6. 1 tsp vanilla
  7. Dash sea salt
Heart Toppers
  1. 1 1/2 cup dark chocolate of choice
Cupcake Directions
  1. Preheat oven to 350
  2. In a mixing bowl combine dry ingredients, excluding the chocolate chunks
  3. Add in wet ingredients and whisk together
  4. Add in chocolate chips
  5. Pour into muffin liners halfway
  6. Bake on 350 for 15-20 minutes, or until a toothpick comes out clean
  7. Let cool completely before frosting
Frosting Directions
  1. Cream softened butter until fluffy
  2. Add in full-fat coconut milk until light and fluffy
  3. Add in vanilla and melted chocolate
  4. Add in cocoa powder and powder sugar until frosting is light, fluffy, and whipped
  5. Frost cupcakes
  6. Store frosting in the refrigerator and let come to room temperature before using
Heart Toppers Directions
  1. Line a baking sheet with parchment paper
  2. Melt chocolate and draw hearts, letters, etc.*
  3. Gently stick toppers into frosting
  4. Store in the refrigerator; bring to room temperature before serving
  1. *I use these squeeze bottles to draw the hearts and letters, you can do it without, though!
Lexi's Clean Kitchen