Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a large bowl, whisk together the all-purpose flour, cocoa powder, baking powder, baking soda, salt, granulated sugar, and brown sugar until well combined.
In a separate medium bowl, beat the eggs. Add the Greek yogurt, vegetable oil, vanilla extract, and milk. Mix until smooth.
Add the wet ingredients to the dry ingredients and stir until just combined.
Fold in the cooked quinoa and semisweet chocolate chips gently until evenly distributed.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the pan for 5 minutes.
Transfer the muffins to a wire rack to cool completely before serving.