It has been reported that during the first few days following entry to a kennel environment, shelter dogs may suffer poor welfare. Previous work suggests that motor bias (the preferred use of one limb over the other) can potentially be used as an indicator of emotional reactivity and welfare risk. In this study, we investigate whether paw preference could be used as a predictive indicator of stress coping (measured using cortisol levels and behavioural observation) in a sample of 41 dogs entering a rescue shelter. Cortisol levels and behavioural observations were collected for one week after admission. We scored the dogs’ paw preference during a food-retrieval task. Our results showed that increasing left-pawedness was associated with a higher expression of stress-related behaviours such as frequent change of state, vocalisations and lower body posture. These results are in keeping with previous findings showing that left-limb biased animals are more vulnerable to stress. Paw preference testing may be a useful tool for detecting different coping strategies in dogs entering a kennel environment and identifying target individuals at risk of reduced welfare.