Line a 12-cavity muffin tin with paper muffins liners and set aside.
Place the chocolate chips in a medium microwave-safe bowl, melt in the microwave using 30-second intervals until the chocolate is fully melted. Add 1/4 cup peanut butter and whisk to combine.
Add about 2 teaspoons of melted chocolate mixture to each muffin liner. Use a silicone pastry brush or the back of a spoon to spread the chocolate about ⅓ of the way up the muffin liner to form the base of the chocolate cup. Make sure the bottoms of the cups are smoothed into an even layer, then place in the freezer to firm up for 10 minutes.
While the chocolate sets up, in a medium bowl, combine 3/4 cup peanut butter, oat flour (if using), and maple syrup until smooth. When the chocolate is firm, place 1 tablespoon of peanut butter into each chocolate cup. Use an offset spatula to smooth the peanut butter into a single layer. Place in the freezer to firm up for 10 minutes.
Add about 2 teaspoons of the remaining chocolate on top of each chocolate cup. Use the back of a spoon to spread the chocolate into an even layer. Sprinkle the tops with flaky salt (if desired), then place back in the freezer for an additional 10 to 20 minutes.
Notes
Storage: It’s best to store homemade peanut butter cups in an airtight container in the refrigerator. This will help keep the chocolate from melting. They will keep for up to 5 days.Freezing: To freeze peanut butter cups, place them in an airtight container and place them in the freezer. They will keep for up to 1 month. Thaw at room temperature for a few minutes before eating.