Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a medium saucepan, combine the rinsed quinoa and water. Bring to a boil over medium-high heat, then reduce heat to low, cover, and simmer for 15 minutes or until the quinoa is tender and water is absorbed. Remove from heat and let cool slightly.
In a large bowl, whisk together the cocoa powder, baking powder, baking soda, salt, and granulated sugar.
In a separate bowl, beat the eggs. Add the vegetable oil, vanilla extract, and Greek yogurt, mixing well.
Add the cooked 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 mini semisweet chocolate chips.
Divide the batter evenly among the prepared muffin cups, filling each about 3/4 full.
Bake 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 before transferring to a wire rack to cool completely.