In a medium bowl, whisk together the almond flour, protein powder, and salt.
Add the maple syrup, vanilla, and melted coconut oil. Stir a bit and then fold in the mini chocolate chips. If the dough feels too wet, add a little more flour. If it feels too dry add a teaspoon of milk at a time.
Portion about a tablespoon or 16 grams of dough into each mini muffin cavity, pressing it down to fill the cup.
Melt the chocolate chips with the coconut oil in 20-second intervals stirring until smooth.
Spoon about half a tablespoon over each cookie dough bite and gently tap the pan so the chocolate settles into an even layer. If there is any extra chocolate evenly disperse it over each cookie bite.
Sprinkle with flaky sea salt if desired and refrigerate for 30-45 minutes or until the chocolate is completely set.
Store in the refrigerator for up to one week or freeze up to 3 months.