The COVID-19 pandemic had significant impacts on the mental health and academic experiences of healthcare trainees. Building on findings from earlier in the pandemic, we explore the impacts on healthcare trainees after a sustained pandemic period of 12–14 months, involving multiple lockdowns, changes in government COVID-19 regulations and the delivery of health education. A qualitative study was conducted between March–May 2021. Participants were 12 healthcare trainees (10 women, 2 men) of medicine, nursing, and midwifery, registered at one of three higher education institutions in the United Kingdom. Interviews were fully transcribed, and data were thematically analysed using a combination of deductive and inductive approaches. We identified three key themes with eight subthemes: (i) academic experiences (adjustment to online learning, loss of clinical experience, confidence in the university), (ii) impacts on wellbeing (psychosocial impacts, physical impacts, pandemic duration and multiple lockdowns), and (iii) support frameworks (university preparedness for increased student support needs, importance of relationship with academic tutors). Findings shed light on the long-lasting and emerging impacts of the pandemic over time. We identify support needs for trainees both during their academic studies, and as they move forwards into professional roles within the healthcare workforce. Recommendations are made for higher education institutions and healthcare employers.