Line your mini muffin tin with paper liners or silicone molds to prepare for layering.
Melt the chocolate gently using a double boiler or microwave, heating in short bursts and stirring until smooth and glossy. The aroma should be warm and nutty, and the chocolate will be silky to the touch.
Pour a small spoonful of melted chocolate into each cup, tilting the tin gently to cover the bottom evenly. Chill in the fridge for about 5 minutes until the chocolate firms up slightly.
While the chocolate sets, mix the peanut butter with honey, a pinch of salt, and vanilla extract in a bowl. Warm the mixture slightly if it feels too thick, until it becomes smooth and easy to scoop.
Drop about a teaspoon of the peanut butter mixture into the center of each chocolate layer, gently pressing it down to spread evenly without overflowing the edges.
Cover the peanut butter layer with more melted chocolate, spooning or pouring to fully enclose the filling. Lightly tap the tray to settle the layers and smooth the tops.
Sprinkle a tiny pinch of flaky sea salt on top of each cup for a flavor contrast, then place the tray back in the fridge. Chill for at least 1 hour until the chocolate is fully set and glossy.
Once chilled, remove the cups from the fridge and let them sit at room temperature for about 5 minutes before serving to enhance their shine and texture.