Preheat the oven to 425 degrees F and line a 12-cup muffin pan with paper liners.
Whisk the all-purpose flour, cocoa powder, granulated sugar, baking powder, baking soda, fine salt, and espresso powder in a large bowl.
Whisk the yogurt, whole milk, neutral oil, and vanilla extract in a separate bowl until completely smooth.
Add the wet mixture to the dry ingredients and fold until only a few flour streaks remain. Fold in 1 cup of the semisweet chocolate chips without overmixing.
Divide the thick batter evenly among the 12 muffin cups and scatter the remaining chocolate chips over the tops.
Bake for 5 minutes, then reduce the oven temperature to 350 degrees F without opening the door. Continue baking for 14 to 17 minutes, until the muffin tops spring back when gently pressed.
Cool the muffins in the pan for 10 minutes, then transfer them to a cooling rack. Let them cool for at least 15 minutes so the tender centers can set.
