Preheat oven to 350F. Line a 12 cup muffin pan with silicone or paper cupcake liners.
In a medium bowl, whisk together the cocoa powder, baking powder, baking soda and salt until smooth. Set aside.
Add the Greek yogurt, maple syrup, eggs, oil and vanilla to a large mixing bowl. Using a hand blender, blend until combined. Add ¼ cup of the quinoa and blend until mostly smooth. Repeat adding ¼ cup quinoa, pureeing each time until all the quinoa has been added.
Add the dry ingredients to the large bowl with the quinoa. Stir just until blended.
Let the cupcake batter sit for 10 minutes (this is important!)
Then divide batter between the cupcake pan. Bake for 19 minutes or until a toothpick inserted in the center of a cupcake comes out clean. Set aside to cool.
Top cupcakes with gluten-free chocolate icing and enjoy. Sprinkle with chopped pistachios if you want!