Line a standard mini muffin tin with 12 paper liners.
Combine dark chocolate chips and 1 tablespoon of coconut oil in a microwave-safe glass bowl.
Heat the chocolate mixture in 30-second intervals, stirring between each, until the texture is completely smooth and liquid.
Spoon approximately 1 teaspoon of the melted chocolate into the bottom of each muffin liner and rotate the tin to ensure the base is evenly coated.
Place the tin in the freezer for 10 minutes to allow the base layer to solidify.
In a small mixing bowl, whisk together the natural peanut butter, maple syrup, and the remaining 1 tablespoon of coconut oil until a homogeneous paste forms.
Remove the tin from the freezer and distribute the peanut butter mixture evenly among the 12 liners, placing it in the center of the chocolate base.
Spoon the remaining melted chocolate over the peanut butter layer, ensuring the edges are sealed and the top is smooth.
Sprinkle a small amount of flaky sea salt onto the center of each cup.
Freeze the assembly for at least 60 minutes until the chocolate is firm and the center is set.