The transportation of mice into a new clean cage after surgery is a standard procedure but might have detrimental effects during the critical post-surgical recovery phase. To analyse the effect of post-surgical housing, female C57BL/6J mice housed in their familiar home cage or in a new environment after minor surgery ± analgesia, anaesthesia only or no treatment were monitored using non-invasive methods during the immediate postsurgical period to assess pain and general impairment. Behavioural investigations and burrowing test revealed no significant differences between housing conditions in untreated mice. While no appearance or posture abnormalities were observed post-experiment, home cage behaviours were affected distinctly. Behavioural rhythmicity was disrupted, and behaviours related to well-being, such as burrowing performance, were less compared to untreated mice. Burrowing latency ranged from an intermediate level following anaesthesia only and surgery with analgesia, to pronounced prolongation after surgery without analgesia in animals housed in their home cage, while after all experimental treatments burrowing latency in animals in new cages was prolonged dramatically. General activity and climbing behaviour in treatment groups housed in new cages tend to be higher compared to animals in familiar cages, leading to significant interactions between housing and treatment conditions (p = 0.006; p = 0.014). These behavioural differences in animals housed in a new environment compared to animals housed in their familiar environment might be interpreted as signs of reduced well-being, agitation and restlessness in the new cages and may hint that animals cope better with surgical stress when housed in their familiar environment. The post-surgical transport to a new and clean cage might therefore be an additional stressor after an exhausting event and may affect recovery.