Preheat oven to 350°F and line a cupcake pan with 12 cupcake liners.
In a large mixing bowl, combine the almond flour, tapioca flour, baking soda, baking powder, salt, coconut sugar, and cacao powder. Whisk all dry ingredients together.
2 cups (196g) blanched almond flour, ½ cup (57g) tapioca flour, ¾ tsp baking powder, ¾ tsp baking soda, 1½ tsp kosher salt, 1 cup coconut sugar, ⅔ cup (66g) cacao powder
In a separate mixing bowl or large liquid measuring cup, whisk the milk, applesauce, coconut oil, and melted chocolate. If the coconut oil or chocolate firms up at all, warm the mixture for about 20 seconds to re-liquify the mixture. Whisk in the nut butter, eggs or flax eggs, and vanilla extract.
½ cup (4 oz) non-dairy milk of choice, ⅓ cup (81g) unsweetened applesauce, ¼ cup (50g) refined coconut oil, ¼ cup (1.5 oz) dark chocolate, ¼ cup (64g) creamy almond or cashew butter, 1 large egg + 1 yolk room temperature or 2 flax eggs, 2 tsp pure vanilla extract
Pour the wet ingredients into the mixing bowl with the dry ingredients and stir until fully combined.
Divide the batter between the 12 cupcake liners; they’ll be about 2/3 full. Bake for 18 to 20 minutes or until a toothpick inserted into the center comes out clean and the top springs back when pressed. Let cool completely.