Abstract Background Approximately a quarter of Australian children are classified as overweight or obese. In high-income countries, childhood obesity follows a socio-economic gradient, with greater prevalence amongst the most socio-economically disadvantaged children. Community-based interventions (CBI), particularly those using a systems approach, have been shown to be effective on weight and weight-related behaviours. They are also thought to have an equitable impacts, however there is limited evidence of their effectiveness in achieving this goal. Methods Secondary analysis was conducted on data collected from primary school children (aged 6–13 years) residing in ten communities (five intervention, five control) involved in the Whole of Systems Trial of Prevention Strategies for Childhood Obesity (WHO STOPS) cluster randomised trial in Victoria, Australia. Outcomes included Body Mass Index z-score (BMI-z) derived from measured height and weight, self-reported physical activity and dietary behaviours and health related quality of life (HRQoL). Repeat cross-sectional data from 2015 (n = 1790) and 2019 (n = 2137) were analysed, stratified by high or low socio-economic position (SEP). Multilevel linear models and generalised estimating equations were fitted to assess whether SEP modified the intervention effect on the outcomes. Results There were no overall changes in BMI-z for either SEP strata. For behavioural outcomes, the intervention resulted in a 22.5% (95% CI 5.1, 39.9) point greater improvement in high-SEP compared to low-SEP intervention schools for meeting physical activity guidelines. There were also positive dietary intervention effects for high SEP students, reducing takeaway and packaged snack consumption, although there was no significant difference in effect between high and low SEP students. There were positive intervention effects for HRQoL, whereby scores declined in control communities with no change in intervention communities, and this did not differ by SEP. Conclusion The WHO STOPS intervention had differential effects on several weight-related behaviours according to SEP, including physical activity. Similar impacts on HRQoL outcomes were found between high and low SEP groups. Importantly, the trial evaluation was not powered to detect subgroup differences. Future evaluations of CBIs should be designed with an equity lens, to understand if and how these types of interventions can benefit all community members, regardless of their social and economic resources.