In a large slow cooker, combine the onions, carrots, garlic, pureed chipotles in adobo, tomatoes, chili powder, cumin, and salt. Add the beans and stir to combine, then stir in the chicken.
Cook in the slow cooker on high for 4 hours. Stir in the chopped scallions and the lime juice right before serving. Serve with shredded cheese and sour cream on the side and let everyone top their own bowls as they wish.