Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a medium bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking powder, baking soda, and salt until well combined.
In a large bowl, beat the granulated sugar, brown sugar, and eggs together until smooth and creamy.
Add the vegetable oil, vanilla extract, and Greek yogurt to the sugar and egg mixture. Mix until fully incorporated.
Fold the grated zucchini into the wet ingredients.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined. Do not overmix.
Fold in the semi-sweet chocolate chips evenly.
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 and let them cool completely before serving.