Preheat and prep. Heat your oven to 350°F (175°C).
Line a 12-cup muffin tin with liners or grease lightly.
Mix the wet ingredients. In a large bowl, whisk the peanut butter, eggs, milk, maple syrup (or honey), and vanilla until smooth. If your peanut butter is very thick, warm it slightly so it blends easily.
Combine the dry ingredients. In a separate bowl, stir together the flour, protein powder, cocoa powder, baking powder, baking soda, and salt. Break up any cocoa or protein powder clumps with a whisk.
Bring it together. Add the dry mixture to the wet mixture.
Stir gently with a spatula just until combined. If the batter seems too thick (like cookie dough), add milk 1 tablespoon at a time until it looks like a thick, scoopable muffin batter.
Fold in chocolate chips. If using, stir in the mini chocolate chips, reserving a few for the tops.
Fill the pan. Divide the batter evenly among the muffin cups, about 3/4 full. Sprinkle the reserved chips on top for a bakery look.
Bake. Bake for 16–20 minutes, or until the tops spring back lightly when touched and a toothpick comes out with a few moist crumbs.
Cool. Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack.
Cool completely if you plan to store or freeze them.