Preheat and prep: Heat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Mix dry ingredients: In a large bowl, whisk flour, cocoa powder, protein powder, sugar, baking powder, baking soda, and salt until no lumps remain. If using espresso powder or flaxseed meal, whisk them in now.
Combine wet ingredients: In a separate bowl or large measuring cup, whisk eggs, milk, yogurt, oil, and vanilla until smooth.
Bring it together: Pour wet ingredients into the dry. Stir gently with a spatula just until combined. Do not overmix; a few streaks are fine.
Add chocolate: Fold in chocolate chips.
The batter will be thick but scoopable.
Fill the pan: Divide the batter evenly among the 12 cups, filling each about 3/4 full. For taller domes, you can slightly overfill.
Bake: Place on the middle rack and bake for 16–20 minutes. They’re done when a toothpick comes out with a few moist crumbs but no wet batter.
Cool: Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool.
Enjoy warm or at room temperature.