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Introduction Physical inactivity is a pressing global health issue. Health professionals have valuable opportunities to promote physical activity to patients across the lifespan, but they report barriers to providing such guidance. The Promotion of Physical Activity by Health Professionals trial aims to deliver implementation strategies to teams of health professionals (n=30 clusters) to address barriers and leverage facilitators within their clinical context to promote physical activity among their patients (n=720) (individuals aged five or above receiving care in outpatient or private settings). This trial will use a hybrid type 1 effectiveness-implementation design to investigate the effect of this support on moderate-to-vigorous physical activity (MVPA) in patient participants compared with a waitlist control. In addition to determining the effectiveness of this physical activity promotion approach, we will conduct a process evaluation that explores implementation within the trial and seeks to identify mechanisms that help explain the findings.Methods Our mixed methods process evaluation will employ measures to address determinants across implementation and intervention delivery, guided by a logic model which articulates how the implementation strategies and intervention are intended to work. This is informed by the UK Medical Research Council’s guidance on process evaluations for complex interventions and McKay’s implementation evaluation roadmap. Data will be collected using surveys and interviews with participating health professionals and patients. Implementation outcomes will include adoption, reach, fidelity and dose. Implementation determinants will include feasibility and acceptability. Quantitative data will be summarised using descriptive statistics and presented using tables and narrative synthesis. Qualitative data will be analysed using a qualitative descriptive approach. Later stage qualitative analysis will incorporate emergent findings from the quantitative analysis to develop a nuanced picture combining narrative accounts with descriptive statistics, exploring how and why implementation support influenced key drivers of behaviour change.Discussion Results of this process evaluation will improve understanding of implementation within the study and mechanisms which may impact MVPA among patient participants. This evaluation aims to guide future implementation and scale-up of the implementation strategies and interventions to suit varied clinical contexts and future research.Trial registration number Australian New Zealand Clinical Trials Registry (ACTRN12623000920695).