Preheat oven to 350 degrees F.
Grease or line 24 muffin tins with paper liners and set aside.
In a large bowl, combine the flour, cocoa powder, sugar, baking powder, baking soda, and salt. Whisk together until well mixed. In another bowl, combine the Greek yogurt and eggs. Whisk to break up the eggs, then add the melted butter and whisk again.
Add the flour mixture into the yogurt mixture and fold with a rubber spatula until almost completely mixed, then carefully fold in 1½ cups of the chocolate chips and mix completely. The batter will be stiff.
Using an ice cream scoop or spoon, fill the muffin tins 3/4 full, then sprinkle the remaining 1/2 cup of chocolate chips over the tops.
Bake in your preheated oven for 22-25 minutes, or until a toothpick inserted into the center comes out clean.
Remove from the oven and let cool for about 5 minutes, then remove the muffins to cool completely on a wire rack. Enjoy!