In a large bowl, combine ghee and coconut sugar until creamy and well mixed. Add in the egg and vanilla and stir well.
Add in the almond flour, tapioca flour, salt, and baking soda. Mix well until no dry spots remain and batter is smooth. Fold in chocolate chips. Cover and refrigerate at least 1 hour or up to overnight.
Preheat oven to 350° and line 2 cookie sheets with parchment paper.
Remove the dough from the fridge and divide into 22 equal balls. Each ball should be about a heaping tablespoon. 11 will fit on each sheet. Roll each ball and evenly space them apart on the sheet. Add more chocolate chips on top if desired.
Bake for 12-13 minutes. Let cool before removing them. They will be soft in the center until cool. Bake a couple extra minutes for a crunchier cookie.
Store in an airtight container at room temperature for 2 days and in the fridge after that.