Combine almond flour, eggs, baking powder, salt, honey, and cocoa powder in a blender. Blend until smooth. Pour mixture into 9 muffin cups (we used silicone for testing purposes).
Bake at 425 for 15 minutes. (Cupcakes are done when dry to the touch and spring back when lightly pressed.)
Allow to cool.
Filling
Combine cream cheese, honey, and milk in a blender. Blend until smooth. Place 1/3 the mixture into a piping bag fitted with a cone tip. Insert cone into the center of one cupcake. Squeeze about 1 tablespoon filling into cupcake. Repeat with remaining cupcakes.
Topping
Add cocoa powder to remaining cream cheese mixture. Blend well. Spread mixture evenly over each cupcake, covering the holes made by the filling.