Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease the wells.
In a large bowl, whisk the yogurt, eggs, maple syrup, brown sugar, oil, vanilla, and milk until smooth.
The mixture should be glossy and lump-free.
In a separate bowl, whisk the protein powder, flour, cocoa powder, baking powder, baking soda, and salt. Break up any cocoa or protein clumps with the whisk.
Pour the dry ingredients into the wet ingredients. Gently fold with a spatula until just combined. Do not overmix; a few streaks are fine.
Fold in the chocolate chips and any optional add-ins.
The batter will be thick but scoopable.
Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle a few extra chips on top if you like.
Bake for 16–20 minutes, or until the tops spring back and a toothpick comes out with a few moist crumbs. Avoid baking until totally dry or they’ll be tough.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. The muffins set up as they cool, so give them a little time.