01 - Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease with oil.
02 - In a large mixing bowl, whisk together whole wheat flour, cocoa powder, protein powder, baking powder, baking soda, and salt.
03 - In a separate bowl, beat together the eggs, applesauce, Greek yogurt, honey (or maple syrup), milk, vanilla extract, and melted coconut oil until smooth.
04 - Pour the wet ingredients into the bowl with the dry ingredients. Stir gently until just combined; avoid overmixing.
05 - Gently fold in the dark chocolate chips, if using.
06 - Divide the batter evenly among the 12 prepared muffin cups.
07 - Bake for 18 to 22 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs.
08 - Allow muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.