Prep the pan and oven. Heat the oven to 400°F (200°C).
Line a 12-cup muffin pan with paper liners or grease well. A hotter oven at the start helps create tall, rounded tops.
Mix the dry ingredients. In a large bowl, whisk together flour, cocoa powder, sugar, baking powder, baking soda, and salt until evenly combined and no cocoa lumps remain.
Mix the wet ingredients. In a separate bowl or large measuring cup, whisk eggs, milk, oil, yogurt or sour cream, vanilla, and coffee (if using) until smooth.
Combine gently. Pour the wet mixture into the dry ingredients. Stir with a spatula until just combined.
The batter should be thick and slightly lumpy. Do not overmix.
Add the chocolate. Fold in about 1 cup of the chocolate chips or chunks, saving the rest for topping.
Fill the cups. Divide the batter evenly among the muffin cups, filling them almost to the top. Sprinkle the remaining chocolate over each muffin. Add a pinch of coarse sugar if you like a slight crunch.
Bake high, then lower. Bake at 400°F (200°C) for 5 minutes, then reduce the oven to 350°F (175°C) without opening the door.
Continue baking 12–14 more minutes, or until a toothpick comes out with a few moist crumbs (melted chocolate is fine).
Cool just a bit. Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack. Enjoy warm or at room temperature.