The coronavirus 2019 (Covid-19) pandemic has given rise to significant global challenges across education, and specifically in the physical education teacher education (PETE) community. Students attending teacher education programmes during the Covid-19 pandemic have experienced an abrupt and unprecedented pedagogical transition from a face-to-face capacity to remote teaching, learning, and assessment environments. Crucially, student teachers’ school placement experiences faced increased challenges and practical implications from additional environmental and social changes. In the context of continued global and national challenges for initial teacher education (ITE) programmes, the present qualitative study, using a representative sample of 24 student physical education (PE) teachers from a PETE programme, investigates the perceived implications of the Covid-19 pandemic on student teachers’ practice and wellbeing during their final 2020/2021 academic year. Results indicate that student teachers maintain that exercise, connections with the university and school placement communities, alongside personal and professional organisation skills serve as resilience resources protecting their wellbeing. Conversely, student teachers express that school placement isolation, restricted PE delivery, increased workload, low teacher efficacy, and the responsibility to implement Covid-19 behaviour regulations presented as challenges that negatively affect their wellbeing. The paper concludes with practices that may further support PETE and ITE programmes and their student teachers to maintain a stable level of wellbeing throughout their careers.