Line a 12-cup mini-muffin pan with 12 mini-muffin liners.
Place the chocolate chips and coconut oil in a microwave-safe bowl. Microwave at 50% power in 30-second intervals, stirring well between intervals, until the chocolate is completely melted and smooth.
Spoon a very thin layer of the melted chocolate into the bottom of each lined muffin cup (just enough to cover the bottom). Tap the pan gently on the counter to level the chocolate.
Transfer the pan to the freezer for 5–10 minutes, until the chocolate layer is firm.
While the chocolate is chilling, combine the natural creamy peanut butter and the vanilla protein powder in a bowl. Stir or knead until evenly mixed and a cohesive dough forms. Divide the mixture into 12 equal portions and roll each portion into a small ball (roughly teaspoon-sized).
Remove the muffin pan from the freezer. Place one peanut butter ball into the center of each chocolate-lined cup and press each ball flat with your fingers or the back of a spoon, leaving a small chocolate rim visible around the edge.
Reheat the remaining chocolate if it has started to set: microwave at 50% power in 15-second intervals, stirring between intervals, until smooth.
Spoon the melted chocolate over each peanut-butter-filled cup to fully cover the filling and seal the edges. Smooth the tops as needed.
Cover the pan with plastic wrap and refrigerate for 30 minutes to 1 hour, until the cups are fully set.
Let the peanut butter cups sit at room temperature for a few minutes before serving, or store them in a sealed container in the refrigerator until ready to eat.