Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a large bowl, whisk together the all-purpose flour, unsweetened 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 vegetable oil, vanilla extract, and milk, whisking until smooth.
Add the cooked and cooled quinoa to the wet ingredients and stir to combine.
Pour the wet ingredients into the dry ingredients and gently fold together until just combined. Do not overmix.
Fold in the semi-sweet chocolate chips evenly into the batter.
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.