Preheat oven to 350 F. Prepare the "vegan buttermilk" by mixing together the coconut milk and apple cider vinegar. Set aside.
In a large mixing bowl or in the bowl of your stand mixer, beat the eggs, coconut sugar, coconut oil, and vanilla together until light and creamy. Add the coconut milk and apple cider vinegar and beat again to incorporate.
Fold in the almond flour, tapioca flour, cacao powder, baking powder, and baking soda until no flour clumps remain. Be sure not to over mix this step.
Pour in the warm coffee and fold into the batter with a rubber spatula.
Use a cookie scoop to pout the batter into a cupcake tin lined with liners and bake for 15 - 18 minutes. Let cool before icing.
Once cool, fill a pipping bag fitted with a star tip with the chocolate ganche. Swirl the frosting on top of each cupcake. Store in the fridge until ready to enjoy.