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Preheat oven to 350 degrees. In a bowl combine applesauce, eggs, nut butter, honey and ghee. Whisk until evenly blended.
Add in coconut flour, almond flour, cacao powder, baking soda, baking powder, vanilla and salt. Blend again until completely combined.
Add in chocolate chunks and stir to combine once or twice just to incorporate.
Pour into cupcake liners and top with a few extra chocolate chunks.
Bake for 15 - 18 minutes or until a toothpick inserted comes out with just few crumbles.