Place cupcake liners into each section of a muffin tin or silicone muffin tray. Make sure the liners sit flat against the sides so the chocolate layers form evenly. Silicone liners work especially well because the fudge cups release more easily after chilling, but regular paper liners also work perfectly. If you want smaller, bite-sized portions, you can use a mini muffin tray instead.

Add the sugar-free chocolate chips and coconut oil to a microwave-safe bowl. Heat in short 20-second intervals, stirring thoroughly after each round until the chocolate becomes completely smooth, glossy, and silky. Be patient during this step because sugar-free chocolate can burn quickly if overheated. If the chocolate looks thick, continue stirring for a few seconds before reheating since the residual warmth often finishes melting it naturally.

Spoon a small layer of melted chocolate into the bottom of each cupcake liner. Use the back of a spoon to gently spread the chocolate slightly up the sides to create a cup shape that will hold the peanut butter filling later. Try to keep the layer even so the cups set properly. Place the tray into the freezer for about 10 minutes, or until the chocolate feels firm to the touch. This quick chill helps create clean layers and prevents the filling from sinking.

While the chocolate layer chills, prepare the peanut butter filling. In a mixing bowl, combine the peanut butter, protein powder, Greek yogurt, powdered sweetener, vanilla extract, and a pinch of salt. Stir slowly at first, then continue mixing until the filling becomes thick, creamy, and completely smooth. The texture should resemble soft fudge. If the mixture feels too dry, add a small spoonful of yogurt. If it feels too soft, let it rest for a minute so the protein powder can absorb some moisture naturally.

Remove the muffin tray from the freezer and spoon the peanut butter filling evenly into each chocolate shell. Gently press the filling down with the back of a spoon so there are no large air pockets. Leave a little room at the top of each cup for the final chocolate layer. Don’t worry if they don’t look perfectly smooth — the top chocolate layer will help everything come together beautifully.

Spoon the remaining melted chocolate over the top of each filled cup until the peanut butter layer is completely covered. Gently tap the muffin tray on the counter a few times to smooth the tops and help the chocolate settle evenly around the filling. If you’d like, sprinkle a tiny pinch of flaky sea salt or crushed peanuts on top before chilling for extra flavor and texture.

Place the tray into the refrigerator for about 2 hours or freeze for 30–40 minutes until the fudge cups are completely firm and set. Once chilled, remove the liners carefully and serve cold for the best creamy texture. If frozen solid, let the cups sit at room temperature for a few minutes before eating so the filling softens slightly and becomes extra smooth and rich.