Background Ongoing concern for the unique mental health challenges faced by university students has been magnified by the disruption of the global COVID-19 pandemic since March 2020. Aims This study aimed to investigate changes in mental health and wellbeing outcomes for UK university students since the pandemic began, and to examine whether more vulnerable groups were disproportionately impacted. Methods Students at a UK university responded to anonymous online cross-sectional surveys in 2019 (N = 2637), 2020 (N = 3693), and 2021 (N = 2772). Students completed measures of depression, anxiety and subjective wellbeing (SWB). Multivariable logistic regression models investigated associations of survey year and sociodemographic characteristics with mental health and SWB. Results Compared to 2019, fewer students showed high levels of depression and anxiety symptoms in 2020. However, there was evidence of worsened levels of anxiety and SWB in 2021 compared to 2019. Interaction effects indicated that students from a Black, Asian or minority ethnicity background and students previously diagnosed with a mental health difficulty showed improved outcomes in 2021 compared to previous years. Conclusions There is a need for sector-wide strategies including preventative approaches, appropriate treatment options for students already experiencing difficulties and ongoing monitoring post-pandemic.