Preheat oven to 350 degrees Fahrenheit and lightly add 12 cupcake liners to a pan.
To a bowl, mix the flax and almond milk and allow to sit in the fridge for 15 minutes.
To a stand mixer, mix the almond flour, cocoa, coconut flour, baking soda, and salt. Add in the maple, butter and the flax eggs and continue to mix until well incorporated. Manually mix in the chocolate pieces and the vanilla extract.
Divide between the cupcake liners and bake for about 15-20 minutes, until dry on the top. Allow to cool completely to room temperature.
Meanwhile, place a bowl over a small saucepot filled with 1 inch of simmering water. Place the coconut milk and dark chocolate in the bowl and stir slowly until melted. Remove from the heat.
Once the cupcakes are cool, dip them into the chocolate ganache and top with almonds.