Heat the oven to 425°F. Line a 12-cup muffin pan with paper liners.
Whisk the all-purpose flour, baking powder, baking soda, fine salt, and granulated sugar together in a large bowl.
In a second bowl, whisk the Greek yogurt, whole milk, melted butter, and vanilla extract until smooth.
Fold the wet mixture into the dry ingredients just until a few flour streaks remain. Fold in 1 cup of the chocolate chips, taking care not to overmix.
Divide the batter evenly among the muffin cups, filling them nearly to the top. Scatter the remaining chocolate chips and the coarse sugar over the batter.
Bake for 5 minutes at 425°F, then reduce the oven to 350°F without opening the door and bake for 14 to 17 minutes more. Cool in the pan for 5 minutes, then transfer the muffins to a rack.
