Background: Process evaluations provide insight into how interventions are delivered across varying contexts and why interventions work in some contexts and not in others. This manuscript outlines the detailed protocol for a process evaluation embedded in a cluster randomised trial of a digital depression prevention intervention delivered to secondary school students (The Future Proofing Study). The purpose of this manuscript is to describe the methods that will be used to capture process evaluation data within this trial. Methods: A mixed methods design will be used for this process evaluation with data collected in the intervention arm of the Future Proofing Study. Data collection methods will include semi-structured interviews with school staff members and study facilitators, automatically collected intervention usage and completion data, and participant questionnaires (completed by school staff, school counsellors, study facilitators, and school students). Information will be collected about: i) how the intervention was implemented in schools, including fidelity; ii) school contextual factors and their association with intervention reach (including completion), uptake and acceptability; iii) how school staff, study facilitators, and students and responded to delivering or completing the intervention. How these factors relate to trial effectiveness outcomes will also be assessed. Overall synthesis of the data will provide school cluster-level and individual-level process outcomes. Discussion: This process evaluation provides a detailed description of how to embed a process evaluation into a trial of a complex intervention in schools. It will provide important information about the Future Proofing Study from the perspectives of key groups necessary for implementation – school-teachers, school counsellors and other school staff, as well as study facilitators and students. An understanding of school contextual factors that hinder or facilitate intervention reach and uptake will be provided. Results will also contextualise the trial findings with respect to how the intervention may have worked in some schools but not in others. Furthermore, this process evaluation will inform the development of a model for rolling out digital interventions for the prevention of mental illness across the school sector. Trial Registration: The randomised controlled trial has been prospectively registered: ACTRN12619000855123. Registered 31 May 2019, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=377664&isReview=trueContributions to the Literature· Process evaluations are critical for understanding how interventions are delivered in real world contexts but are rarely embedded in randomised controlled trials or detailed in prospective protocols. · This protocol is the first to illustrate how to embed a process evaluation into a school-based trial of a digital depression prevention intervention, including the use of flexible and pragmatic quantitative and qualitative data collection methods with key stakeholders. · School context factors will be rigorously assessed and analysed for contribution to intervention reach and completion, uptake of study processes, and clinical outcomes. · Study outcomes will guide sustainability efforts in the delivery of digital depression prevention interventions in schools.