To help you choose vegan foods at their restaurants, Chipotle now has a section indicating what is vegan and what to avoid. See:
https://www.chipotle.com/dietary-options

They say: For the vegans in the bunch, avoiding animal products at Chipotle is easier than you may think. Even without the meats, dairy products, and vinaigrette (which is made with honey), there are still plenty of tasty vegan-friendly options, including our popular Sofritas. The suggested meals (below) contain no animal products.

*Individual foods may come into contact with one another during preparation, which is not reflected in these recommendations. Although we make efforts to separate ingredients in our cooking processes and on our serving line, Chipotle cannot guarantee the complete absence of cross contact with any particular ingredient in any of our food.

See: https://www.chipotle.com/dietary-options

The contents of this posting, website, and our other publications, including Vegetarian Journal, are not intended to provide personal medical advice. Medical advice should be obtained from a qualified health professional. We often depend on product and ingredient information from company statements. It is impossible to be 100% sure about a statement, info can change, people have different views, and mistakes can be made. Please use your best judgment about whether a product is suitable for you. To be sure, do further research or confirmation on your own.

For information about other restaurant chains, see: http://www.vrg.org/fastfoodinfo.php

For information about vegetarian and vegan restaurants in the USA and Canada, see: VRG Online Veggie Restaurant Guide