Preheat the oven to 350°F (175°C) and line a muffin tin with paper liners or grease with cooking spray.
In a large mixing bowl, combine the flour, cocoa powder, baking soda, baking powder, salt, granulated sugar, and brown sugar. Whisk together until well combined.
Add the Greek yogurt, mashed bananas, vegetable oil, eggs, and vanilla extract to the dry ingredients. Stir until just combined, being careful not to overmix.
Fold in the chocolate chips until evenly distributed throughout the batter.
Spoon the batter into the prepared muffin tin, filling each cup about 2/3 full.
Bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.