Preheat oven to 350 degrees F (175 degrees C). Line muffin pans with paper liners.
Combine gluten-free flour, coconut sugar, dark chocolate chips, cocoa powder, coconut flour, baking powder, baking soda, xanthan gum, and salt in a bowl; mix well to combine.
Whisk buttermilk, eggs, vegetable oil, and vanilla extract together in another large bowl until combined. Add flour mixture; fold in with a spatula until completely blended. Divide batter evenly among muffin cups, filling each about halfway.
Bake cupcakes in the preheated oven until a toothpick inserted in the centers comes out clean, about 20 minutes. Cool in pans 5 minutes; transfer to a wire rack to cool completely.