Preheat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or lightly grease with cooking spray.
In a large bowl, sift together the all-purpose flour, cocoa powder, baking powder, baking soda, salt, and granulated sugar. Mix well to combine.
In a separate medium bowl, whisk together the yogurt, eggs, vanilla extract, and milk until smooth.
Pour the wet ingredients into the dry ingredients and gently fold together using a spatula until just combined. Do not overmix; the batter should be slightly lumpy.
Fold in the mini chocolate chips evenly throughout 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 or with a few moist crumbs.
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.