Line a 12-cup muffin pan with paper or silicone muffin liners.
In a medium bowl, combine the peanut butter, honey, flour, and sea salt and stir until well combined, then refrigerate for 5 minutes or until firm enough to shape.
Once the peanut butter mixture has firmed up, scoop 1 tablespoon of the mixture and shape it into a small disk or patty, slightly smaller in diameter than the muffin liner. Repeat until you have 12 patties.
In a heat-safe medium bowl, combine the dark chocolate chips, coconut oil, and vanilla extract and heat over a double boiler or in the microwave for 1-2 minutes, stirring the mixture every 30 seconds or so, until melted and smooth.
Spoon 2 teaspoons of melted chocolate into a muffin liner, spreading it out to cover the bottom, top with a peanut butter patty, and cover with 1 tablespoon of melted chocolate, ensuring it’s completely covered. Then repeat until all 12 muffin liners are full.
Optional: Sprinkle the top of each muffin cup with a pinch of flaky sea salt.
Transfer the muffin tin to the freezer for 15 minutes or to the fridge until all of the chocolate has solidified.
Once solidified, remove them from the fridge or freezer, let sit for 1-2 minutes, remove the wrapper, and enjoy. Any leftovers can be stored in an airtight container in the fridge for one week or in the freezer for 3 months.