Line a muffin pan with 12 muffin liners and set aside.
Add 2/3 cup of the chocolate chips to a microwave safe bowl and microwave in 30 second increments until the chocolate is fully melted.
Fill each muffin liner with ~1 TBS of melted chocolate and swirl with the back of a spoon to coat the sides. Place the pan in the freezer to set.
While the chocolate is freezing, prepare the brownie filling by adding the remaining ingredients (almond flour through peanut butter) to a large mixing bowl and mixing until ingredients form a sticky dough. The mixture should be thick and stick together.
Using a tablespoon, roll the dough between your hands to form individual balls and then flatten them into discs. Place discs into each muffin cup and use your fingers to gently flatten them so they press up against the sides.
Melt the remaining 1/3 cup of chocolate chips the same method as before, then cover the top of the discs with the melted chocolate. Place back in the freezer to set.
Store the cups in an airtight container the fridge for a week or freeze for long-term storage.