Place the quinoa in a dry pan over medium heat. Cook, stirring occasionally, until the quinoa is evenly toasted and beginning to pop, 3 to 4 minutes. Remove from the heat and allow to cool completely.
Add the melted butter, coconut sugar and vanilla extract to a medium bowl. Using a rubber spatula, stir to combine and soften the sugar. Add the egg and egg yolk and stir until smooth. Add the almond flour, coconut flour, baking soda and salt and stir until it forms a soft dough. Add the chocolate chips and quinoa and stir to evenly distribute. Refrigerate for at least 4 hours or up to overnight.
Preheat the oven to 350 degrees F.
Line 2 rimmed baking sheets with parchment paper. Scoop 1/4-cup balls of cookie dough evenly onto the baking sheets leaving 2 inches between each scoop. Flatten them slightly. Bake, rotating halfway through, until the edges are just set and the centers are still slightly underdone, 13 to 15 minutes. Allow to cool for 10 minutes on the baking sheets, then remove to a wire rack to cool completely.
These are best enjoyed the day they are baked, or frozen and eaten straight out of the freezer.