In a microwave safe bowl or measuring glass, melt the chocolate chips, coconut oil and almond butter together. Heat in 15 second increments, stirring every time, until completely smooth. Alternatively, you can melt the ingredients on the stove stop over medium heat.
Add about a teaspoon of the chocolate to each muffin liner and gently tip it to cover some of the side. This should use about half of the chocolate, the remaining will be for the top. Place in fridge or freezer to chill, about 15 minutes.
While the chocolate is chilling, make the cookie dough. In a medium bowl, combine almond butter, maple syrup, coconut oil, almond flour, salt, and vanilla. Stir until well combined. Add in the mini chocolate chips and mix in.
Remove the pan from the freezer and scoop some cookie dough in each compartment as evenly as possible. Top with the remaining chocolate- if it has hardened then place it in the microwave for 10-15 seconds until smooth again. Once all cups are covered with chocolate, place back in the freezer and let harden completely, about 1 hour.