Melt the dark chocolate chips in a microwave-safe bowl in 30-second increments in the microwave, stirring often. Add the coconut oil and stir till the chocolate and oil have melted and are combined.
Place 12 muffin liners on a sheet pan or cutting board. Spoon about two to three teaspoons of melted chocolate into each of the muffin cups. Roll each liner lightly so the chocolate goes up about a quarter inch on the side of the liner.
Refrigerate the tray with the muffin liners for 5 to 10 minutes or until the chocolate has hardened.
Using the back of a spoon, spread a dollop of peanut butter into each muffin cup, distributing it near the edges of the cup.
Top the peanut butter with a small dollop of jelly.
Use the remaining chocolate to top the PB and jelly in each of the cups, and sprinkle a small pinch of flaky sea salt onto each cup.
Refrigerate for 30 minutes or until hardened.