Preheat your oven to 350 and line a muffin pan with paper liners or spray with nonstick spray. Set aside.
In a medium mixing bowl, stir together the cocoa powder, almond flour, baking powder, and salt. Set aside.
In a large mixing bowl, stir together the melted coconut oil, applesauce, coconut sugar, eggs, coffee, and vanilla. Gradually add the dry mixture to the wet and stir just until combined. If batter is too runny, add additional almond flour as needed. Spoon the batter evenly into the muffin liners, about 3/4 full.
Bake for 25 to 30 minutes. A toothpick inserted in the middle should come out mostly clean. There should be a few crumbs stuck to the tooth ick.
Let cool for 5 minutes and then remove to a wire rack to cool completely. Let set for about 2 hours or until completely cool.
For the Frosting
Add all ingredients to a small saucepan, heat to low, and stir until chocolate chips are melted. Allow to cool before spreading over cupcakes. Store frosted cupcakes in an airtight container in the refrigerator.