Background University students’ psychological health is linked to their academic satisfaction. This study aimed to investigate students’ psychological health and academic satisfaction in the context of COVID-19 and academic year-end stress. Methods Standardized self-filled scales for anxiety, depression, stress, psychological well-being, and an ad-hoc COVID-19 stress scale were used in this cross-sectional study. Participants were first- to third-year students of eight different health-related tracks in Geneva, Switzerland. Descriptive statistics and hierarchical regression analyses were applied. Results In June 2020, out of 2835 invited students, 433 (15%) completed the survey. Academic satisfaction was a stronger mental health predictor than COVID-19, which mainly predicted stress and anxiety. Lower academic satisfaction scores were significantly associated with stress (β = -.53, p < .001), depression (β = -.26, p < .001), anxiety (β = -.20, p < .001), while higher scores with psychological well-being (β = .48, p < .001). Being female was strongly associated with anxiety and stress but not with depression or psychological well-being. Lower age was associated with stress only. The nature of the academic training had a lesser impact on mental health and the academic year none. Compared to students starting the academic year, year-end students reported significantly lower academic satisfaction, higher depression, and particularly higher anxiety and stress. There was, however, no difference in psychological well-being. Conclusion Students suffer more from anxiety, stress, depression, and lower satisfaction with studies at the end of the academic year than at the beginning. Academic satisfaction plays a more substantial role than COVID-19 in predicting students’ overall mental health status. Training institutions should address the underlying factors that can enhance students’ academic satisfaction, especially during the COVID-19 period, in addition to ensuring that they have a continuous and adequate learning experience, as well as access to psychosocial services that help them cope with mental distress and enhance their psychological well-being.