Objective: The COVID-19 pandemic has had a significant impact on pupils and staff in English schools. This study aimed to provide an in-depth understanding of the challenges schools faced and the processes they implemented to protect the mental wellbeing of students and staff in the later stages of the pandemic, focusing on January–June 2022. Design: Qualitative study. Setting: Primary and secondary schools in England from April to September 2022. Method: Ten semi-structured interviews were conducted using Zoom with six primary and four secondary school headteachers (or other members of the senior leadership team) in England. Results: Mental wellbeing programming for students and staff was scaled up in both primary and secondary schools amid concerns that the COVID-19 pandemic would impact on mental health. Headteachers perceived changes in the behaviour of students, including increased dysregulation, and staff struggling with fatigue and a sense of being devalued as professionals. Schools scaled up the supports they offered to students and staff, but challenges remain in maintaining such increased support due to the perceived additional needs of staff and students within the context of funding constraints. Despite initial concerns that there would be tension between promoting mental wellbeing and academic catch-up among students, headteachers identified work addressing these two priorities as synergistic. Conclusion: Mental wellbeing impacts of the pandemic on pupils and staff required increased provision of support programmes. Ongoing efforts to monitor the wellbeing needs of students and staff is required. Formal and informal methods to enhance the mental health for pupils and staff should continue into the recovery period.