Preheat the oven to 375°F and line a 12-cup muffin tin with paper liners, then lightly spray the liners with cooking spray.
Roughly chop 12 of the cookies into chunky pieces. Break the remaining 4 cookies into quarters and set aside for the tops.
In a large bowl, whisk together the flour, protein powder, baking powder, baking soda and salt.
Blend the cottage cheese, eggs, sugar, melted butter, milk and vanilla until completely smooth, 30-45 seconds.
Fold the wet mixture into the dry ingredients until a few streaks remain, then fold in the chopped cookies just until combined. Overmixing will turn the batter gray.
Protein powders absorb liquid differently, so if the batter looks very stiff, fold in 1-2 more tablespoons of milk. Divide the batter among the cups and press a cookie quarter into the top of each muffin.
Bake for 18-21 minutes, until lightly golden and a toothpick comes out clean. Cool in the pan for 10 minutes, then move to a wire rack.