Preheat and prep. Heat your oven to 375°F (190°C). Line a 12-cup muffin pan with paper liners or lightly coat with nonstick spray.
Mix dry ingredients. In a medium bowl, whisk flour, cocoa powder, sugar, baking powder, baking soda, and salt until evenly combined.
Mix wet ingredients. In another bowl, whisk Greek yogurt, applesauce, egg whites, and vanilla. If using coffee, add 2 tablespoons now.
Combine. Pour the wet mixture into the dry.
Stir gently with a spatula just until no dry streaks remain. If the batter seems too thick, add another tablespoon of water or coffee. Do not overmix.
Fold in chocolate chips. Reserve a teaspoon to sprinkle on top if you like.
Fold the rest into the batter.
Portion. Divide batter evenly among the 12 muffin cups. Each cup should be about two-thirds full. Sprinkle the reserved chips on top.
Bake. Bake for 10–12 minutes, or until the tops spring back lightly and a toothpick comes out with a few moist crumbs (melted chocolate is fine).
Cool. Let muffins cool in the pan for 5 minutes, then transfer to a rack to cool completely.
This helps set the structure and keeps them tender.