Preheat oven to 325 degrees F and adjust the rack to the middle position. Place the butter and chocolate in a bowl over a double boiler over medium heat. Let the chocolate melt and then cool for 10 minutes.
Place the coconut sugar, vanilla and eggs in a large mixing bowl. Whisk until smooth. Whisk in cooled chocolate mixture.
Sift the coconut flour, tapioca flour, arrowroot, cocoa, salt, baking soda, cinnamon and cayenne over a medium mixing bowl. Add the dry mixture to the wet mixture and stir until combined. Stir in the chocolate chips.
Using a 1 1/2″ cookie scoop, scoop cookie dough onto a baking sheet lined with parchment paper. Bake for 11 minutes.
Note: I only test the recipes on my site with the listed ingredients and measurements. If you would like to try a substitution, you are welcome to share what you used and how it turned out in the comments below. Thanks!