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 got a chicken bowl. The servers took care to change gloves and used different spoons on my ingredients. But they still got the ingredients from the regular line. So cross contamination is possible.
I’m gluten intolerant and have eaten here many times. I tell them I’m gluten intolerant and ask to change gloves. Once recently, the girl seemed confused so I had to ask a few times before she did it, but all of the other times they did it immediately without issue. I always get a rice bowl with chicken so I’m not sure about chips/corn products but I get full off the bowl and eat chips from home. Chip bags are small anyway. It’s a favorite regular place my whole family enjoys and the food is fresh. I haven’t been sick but there is a risk of CC.