Line the pan: Place paper liners in a 12-cup muffin tin. This prevents sticking and makes cleanup easy.
Melt the chocolate base: In a microwave-safe bowl, combine 1 1/2 cups dark chocolate chips with 1 tablespoon coconut oil. Microwave in 20–30 second bursts, stirring between each, until smooth.
Alternatively, melt over a double boiler.
Make the peanut butter filling: In a separate bowl, stir together 3/4 cup creamy peanut butter, 1/4 to 1/3 cup protein powder, 1–2 tablespoons maple syrup or honey, 1–2 tablespoons coconut flour or oat flour, 1/2 teaspoon vanilla, and a pinch of salt. The mixture should be thick but spreadable. Adjust with a splash of milk or a bit more flour as needed.
Create the bottom chocolate layer: Spoon about 1 teaspoon of melted chocolate into each liner and tilt the pan so it coats the bottom.
Place the tin in the freezer for 5–7 minutes to set slightly.
Add the filling: Roll the peanut butter mixture into 12 small disks that are slightly smaller than the muffin cups. Place one disk over each chocolate base and gently flatten. Leave a small border around the edges so the top chocolate can seal the cup.
Top with chocolate: Spoon enough melted chocolate over each cup to fully cover the filling, about 1–1 1/2 teaspoons per cup.
Tap the pan gently on the counter to smooth the tops and release air bubbles.
Add finishing touches: Sprinkle with flaky sea salt or chopped peanuts if you like. This adds crunch and balances sweetness.
Chill to set: Refrigerate for 30–45 minutes or freeze for 15–20 minutes, until the chocolate is firm.
Serve and store: Peel off the liners and enjoy. Keep extras chilled so they hold their shape.