Objectives: This research aimed to explore the health behaviours of health sciences students over time and across different settings. Methods: A health behaviour surveillance system has been implemented in Hamburg and Manchester among under- and postgraduate health sciences students. Trends among the Hamburg sample were described. In a cross-sectional assessment, health behaviours across both universities were examined using multivariate regression analysis. Results: Between 2014 and 2018, increasing trends in physical activity and cannabis and alcohol consumption were observed in Hamburg (n = 1,366). While fruit and vegetable intake was constantly low, tobacco smoking decreased. No clear trend was observed for stress perception. The comparison (n = 474) revealed that Manchester students had higher odds of smoking, excessive alcohol consumption, and fruit and vegetable consumption; and lower odds of being physically active, and consuming cannabis. No difference in stress perception was observed. Conclusions: Varying trends and potential areas of intervention were identified for health behaviours in Hamburg. The comparison with Manchester students revealed differences in behaviours, which could be further explored to help inform health promotion strategies in both settings.