Background: Comprehensive School Health models offer a promising strategy to elicit changes in student health behaviours. To maximise the effect of such models, the active involvement of teachers and students in the change process is recommended. Objective: The goal of this project was to gain insight into the experiences and motivations of teachers and students involved in a choice-based Comprehensive School Health model--Health Promoting Secondary Schools (HPSS). Setting: School communities in British Columbia, Canada. Design and methods: HPSS engaged teachers and students in the planning and implementation of a whole-school health model aimed at improving the physical activity and eating behaviours of high school students. The intervention components were specifically informed by self-determination theory. A total of 23 teachers and 34 school committee members participated in focus group interviews. The minutes of planning meetings were collected throughout the intervention process. Results: Analysis of the data revealed five themes associated with participants' experiences and motivational processes: (a) lack of time for planning and preparation; (b) resources, workshops and collaboration; (c) teacher control impacts student engagement; (d) teacher job action inhibited implementation of HPSS action plans; and (e) choice-based design impacts participants' experiences. Conclusion: Findings from this study can facilitate future school-based projects by providing insights into student and teacher perspectives on the planning and implementation of school-based health promotion programmes and implementing choice-based educational change initiatives.