Preheat oven to 350ºF and line a baking sheet with parchment paper.
Whisk together the flours, cocoa powder, and other dry ingredients (minus the sugar) in a medium mixing bowl and set aside.
Beat together the butter and sugar until fluffy. Beat in remaining wet ingredients.
Add half of the dry ingredients into the wet ingredients and beat together until combined. Add in the rest of the dry ingredients and continue to mix until you have a thick, cookie-like dough. Fold in the chocolate chips and marshmallows.
Scoop the dough onto the baking sheet and gently flatten with your hands (this is optional, but make the cookies more uniform in shape).
Bake in the center of a warm oven for 12 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.