Preheat the oven to 375 degrees F (190 degrees C). Line a muffin pan with 12 muffin liners.
Whisk together flour, baking powder, baking soda, salt, and xanthan gum in a mixing bowl until well combined.
In another large mixing bowl, whisk together sugar, oil, apple cider vinegar, almond milk, and vanilla extract.
Sieve the flour mixture into the wet ingredients. Gently whisk everything together until just combined.
Gently fold in the chocolate chips.
Transfer batter to lined muffin pan. Fill each liner about ⅔ full.
Bake for 18 to 22 minutes, or until a skewer inserted in the center of the muffin comes out clean.