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 it.
Mix dry ingredients. In a large bowl, whisk flour, cocoa, protein powder, sugar, baking powder, baking soda, and salt. Break up any cocoa or protein powder clumps so the batter stays smooth.
Combine wet ingredients. In a separate bowl, whisk eggs, yogurt, milk, oil, and vanilla until well blended. If using espresso powder, add it here so it dissolves evenly.
Bring it together. Pour the wet ingredients into the dry.
Stir gently with a spatula until just combined. A few small lumps are fine. Avoid overmixing, which can make the muffins tough.
Fold in chocolate chips. Save a handful for sprinkling on top.
The contrast of melty chips inside and a few on the surface makes these feel bakery-style.
Fill the cups. Divide the batter evenly among the muffin cups, filling each about 3/4 full. Top with the reserved chips.
Bake. Bake for 16–20 minutes, or until a toothpick comes out with a few moist crumbs. Start checking at 16 minutes; cocoa-based muffins can dry out if overbaked.
Cool. Let the muffins rest in the pan for 5 minutes, then move them to a rack.
Cooling helps the structure set and keeps the crumb tender.