Add 1 cup of dark chocolate to a microwave-safe bowl. Microwave for 2 minutes, stirring every 30 seconds until the chocolate is melted and thin (it might be done earlier depending on power of microwave).
Pour chocolate evenly into bottoms of muffin liners, making sure it spreads evenly. Place muffin tray in freezer and freeze for at least 10 minutes.
In a bowl, mix together peanut butter, almond flour and maple syrup until mixture is thick and cohesive. Remove muffin tray from freezer. Evenly distribute a heaping teaspoon of peanut butter mixture on top of chocolate layer.
Place a teaspoon of jelly on top of peanut butter. Using the back of a spoon, press down gently on the PB&J to flatten them slightly. Place back in freezer for about 5 minutes.
While cups are in the freezer, melt the remaining chocolate.
Remove cups from the freezer and pour melted on chocolate on top, making sure to cover the sides and distribute evenly. Place muffin tray back in freezer for at least 10 minutes.