Prep your pan and oven. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease each cup.
Mix the dry ingredients. In a large bowl, whisk together the flour, cocoa powder, protein powder, baking powder, baking soda, and salt until no clumps remain.
Whisk the wet ingredients. In a separate bowl or large measuring cup, whisk the eggs, Greek yogurt, milk, maple syrup, applesauce, oil, and vanilla until smooth.
Combine gently. Pour the wet mixture into the dry ingredients.
Stir with a spatula until just combined. A few small streaks of flour are okay; avoid overmixing.
Fold in chocolate. Stir in the chocolate chips, reserving a few for topping if you like.
Fill the cups. Divide the batter evenly among the muffin cups, about 3/4 full. Sprinkle the reserved chips on top.
Bake. Bake for 16–20 minutes, or until the centers spring back lightly and a toothpick comes out with a few moist crumbs.
Cool. Let the muffins cool in the pan for 5 minutes, then move them to a wire rack.
Cool fully for the best texture.