Every shelter dog is faced with the challenge to adapt to a kennel environment. To monitor the welfare of individual shelter dogs, evaluating behavioural and physiological parameters, potentially useful as indicators for adaptability of individual dogs is crucial. Nocturnal activity, i.e. resting patterns, has already been identified as a candidate indicator of adaptability and can be easily measured remotely with the help of sensors. We investigated the usefulness of a 3-axial accelerometer (Actigraph®) to monitor nocturnal activity in shelter dogs every night during the full first two weeks in-shelter starting directly at shelter intake, as a measure of welfare. Additionally, urinary cortisol/creatinine ratio (UCCR), body weight and behaviour data were collected to evaluate stress responses. A control group of pet dogs in homes, matched to the shelter dog group, was also monitored. Shelter dogs had higher nocturnal activity and UCCRs than pet dogs, especially during the first days in the shelter. Nocturnal activity, both accelerometer measures and activity behaviour, and UCCRs decreased over nights in the shelter. Smaller dogs had higher nocturnal activity and UCCRs than larger dogs and showed less autogrooming during the first nights. Dogs with no previous kennel experience had higher nocturnal activity and UCCRs, and showed less body shaking, than dogs with previous kennel experience. Overall, sheltered dogs also showed less body shaking during the first night. The number of dogs showing paw lifting decreased over days. Age class and sex effected only few activity behaviours. Shelter dogs significantly lost body weight after 12 days in the shelter compared to the moment of intake. Shelter dogs had disrupted nocturnal resting patterns and UCCRs compared to pet dogs and seem to partly adapt to the shelter environment after two weeks. Sensor-supported identification of nocturnal activity can be a useful additional tool for welfare assessments in animal shelters.