Chipotle does not have a gluten free menu but instead has a list of gluten-containing ingredients to avoid. Cross-contamination is a concern, however, so let the person taking your order know that you are gluten free and if you need them to take the proper precautions.
From their website: "If you avoid gluten, don't eat our flour tortillas. If you are highly sensitive to gluten and would like us to change our gloves, just let us know at the start of your order. You should be aware items containing corn, including corn tortillas (chips, soft corn, and crispy corn tortillas) and corn salsa, may have a small amount of gluten from potentially co-mingling with gluten-containing grains in the field."
I informed them of our gluten allergy and they looked a little confused. He asked if I wanted him to change gloves. I said yes, and the utensils, please. They looked a little annoyed at changing the utensils and they did not wipe anything down. They seemed young and maybe not trained in what to do for a food allergy.
Fantastic experience for Celiacs! This amazing team including Pearson and Kaitlynn, changed all the spoons, changed all the cold food, wiped down the counter, and washed hands & changed gloves for us before preparing our food. This team really understood the needs of celiacs, and did everything they could to avoid cross-contamination to provide the best experience. The food was delicious and fresh. The best chipotle experience we have had in years.