Abstract Background Community-based interventions have shown promise in addressing the childhood obesity epidemic. Such efforts rely on the knowledge of key community members and their engagement with the drivers of obesity in their community. This paper presents the protocol for the measurement and evaluation of knowledge and engagement among community leaders within a whole-of-community systems intervention across 10 large intervention communities in Australia. Methods We will investigate the role of stakeholder knowledge and engagement in the implementation and effectiveness of the stepped wedge cluster randomised trial in ten communities in Victoria, Australia. Data will be collected using the Stakeholder-driven Community Diffusion Survey (SDCD) to measure levels of knowledge and engagement prior to commencement (2019), across the three separate levels of governance within the intervention at five time points. Primary outcomes will be baseline overall knowledge and engagement scores across the three levels of governance and change in overall knowledge and engagement over time. Discussion We hypothesise there will be heterogeneity between intervention sites on levels of knowledge and engagement and that these differences will be associated with variability in implementation success. Trial registration Australian New Zealand Clinical Trials Registry ACTRN12618001986268. Registered on 11 December 2018