Psychological wellbeing in university students is receiving increased focus. However, to date, few longitudinal studies in this population have been conducted. As such, in 2019, we established the Student Wellbeing At Northern England Universities (SWANS) cohort at the University of York, United Kingdom aiming to measure student mental health and wellbeing every six months. Furthermore, the study period included the COVID-19 pandemic, giving an opportunity to track student wellbeing over time, including over the pandemic. Eligible participants were invited to participate via email. Data were collected, using Qualtrics, from September 2019 to April 2021, across five waves (W1 to W5). In total, n = 4,622 students participated in at least one wave of the survey. Data collection included sociodemographic, educational, personality measures, and mental health and wellbeing. Latent profile analyses were performed, exploring trajectories of student wellbeing over the study period for those who had completed at least three of the five waves of the survey (n = 765), as measured by the Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS). Five latent profile trajectories of student wellbeing were identified. Of these, the two latent classes with initially higher wellbeing scores had broadly stable wellbeing across time (total n = 505, 66%). Two classes had lower initial scores, which lowered further across time (total n = 227, 30%). Additionally, a fifth class of students was identified who improved substantially over the study period, from a mean WEMWBS of 30.4 at W1, to 49.4 at W5 (n = 33, 4%). Risk factors for having less favourable wellbeing trajectories generally included identifying as LGBT+, self-declaring a disability, or previously being diagnosed with a mental health condition. Our findings suggest a mixed picture of the effect of the COVID-19 pandemic on student wellbeing, with a majority showing broadly consistent levels of wellbeing across time, a smaller but still substantial group showing a worsening of wellbeing, and a small group that showed a very marked improvement in wellbeing. Those from groups traditionally underrepresented in higher education were most at risk of poorer wellbeing. This raises questions as to whether future support for wellbeing should target specific student subpopulations.