Gather all ingredients.
Place 12 muffin liners in a muffin tin. Spray the liners with cooking spray.
In a microwave safe bowl, add the chocolate chips and coconut oil. Heat in the microwave for about 2 minutes, stirring every 30 seconds. Mix well until the chocolate is melted. Add additional time, if needed.
Scoop a spoonful (about ½ tbsp) of melted chocolate into the bottom of each muffin liner. Use a spoon to press the chocolate up onto the sides a little bit. Set the remaining chocolate aside. (The trick to make the chocolate last is to use less chocolate than you think on the bottom by creating a thin layer and using a spoon to spread it around!)
Place the muffin tin in the freezer for about 10 minutes or until the chocolate is hard.
In another bowl, prepare the peanut butter mixture. Start by adding all of the peanut butter and part of the protein powder. Mix well and continue adding protein powder until the peanut butter mixture isn't drippy anymore. You might need to adjust the ratios based on how drippy the peanut butter is.
Use a small scoop or your hands to make 12 balls with the peanut butter mixture. Set aside. (Note: If you choose to make a drippy mixture, you can place the balls in the freezer to make them a little more firm.)
Once the bottom layer of chocolate is frozen, take the muffin tin out of the freezer. Add one of the peanut butter balls on top of each chocolate bottom and gently use your finger to press the ball so it is smooth on the chocolate.
Use the rest of the melted chocolate to place 2 scoops (about 1 ½ tbsp) over the peanut butter balls to make the top layer of chocolate for the peanut butter cup.
Place the muffin tin in the freezer for another 10 minutes until the chocolate is hard.
Take out of the freezer and enjoy!