Preheat oven to 350ºF and line a baking sheet with parchment paper.
Whisk together the flours, cocoa powder, quinoa flakes and other dry ingredients (minus the sugar) in medium mixing bowl and set aside.
Beat together the coconut oil and sugar until fluffy. Beat in remaining wet ingredients then add to the dry ingredients and stir with a large wooden spoon until you have a thick, cookie-like dough. Fold in the chocolate chips.
Spoon the dough on the parchment lined baking sheet. Smooth over with the back of a wet metal spoon and slightly flatten (this is optional, but make the cookies more uniform in shape). Sprinkle with maldon sea salt if desired.
Bake in the center of a warm oven for 12 - 14 minutes, until the edges are lightly browned and the top of the cookies is still slightly tender to the touch.
Cool on a wire rack for 5 - 10 minutes and enjoy!
Dunk these babies in a glass of almond milk (or regular milk if you so choose) and relish in the chocolatey goodness that you just created.