Preheat oven to 325°. Grease three 12-muffin mini-muffin pans with oil.
In a medium bowl, whisk together flour, potato starch, arrowroot, sugar, baking powder, baking soda, xanthan gum, salt, and unsweetened cocoa powder; set aside.
In a large bowl, mix together applesauce, 1/2 cup canola oil, and vanilla. Slowly add flour mixture, stirring to combine. Stir in coffee until it forms a batter. Fold in chocolate chips.
Place 1 tablespoon batter into each greased muffin cup. Bake until a toothpick inserted into the center comes out clean, approximately 12 to 15 minutes. Let cool completely on a wire rack before removing from tins.