Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or grease well.
In a large bowl, whisk together flour, cocoa powder, baking powder, baking soda, and salt.
In another bowl, mix brown sugar, eggs, yogurt, milk, vegetable oil, and vanilla extract until smooth.
Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix.
Fold in the chocolate chips.
Divide the batter evenly into the muffin cups, filling each about ¾ full.
Bake for 18-22 minutes, or until a toothpick inserted comes out clean.
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.