The Be Active Eat Well (BAEW) community-based child obesity prevention intervention was successful in modestly reducing unhealthy weight gain in primary school children using a multi-strategy and multi-setting approach.To (1) examine the relationship between changes in obesity-related individual, household and school factors and changes in standardised child body mass index (zBMI), and (2) determine if the BAEW intervention moderated these effects.The longitudinal relationships between changes in individual, household and school variables and changes in zBMI were explored using multilevel modelling, with measurement time (baseline and follow-up) at level 1, individual (behaviours, n = 1812) at level 2 and households (n = 1318) and schools (n = 18) as higher levels (environments). The effect of the intervention was tested while controlling for child age, gender and maternal education level.This study confirmed that the BAEW intervention lowered child zBMI compared with the comparison group (-0.085 units, P = 0.03). The variation between household environments was found to be a large contributor to the percentage of unexplained change in child zBMI (59%), compared with contributions from the individual (23%) and school levels (1%). Across both groups, screen time (P = 0.03), sweet drink consumption (P = 0.03) and lack of household rules for television (TV) viewing (P = 0.05) were associated with increased zBMI, whereas there was a non-significant association with the frequency the TV was on during evening meals (P = 0.07). The moderating effect of the intervention was only evident for the relationship between the frequency of TV on during meals and zBMI, however, this effect was modest (P = 0.04).The development of childhood obesity involves multi-factorial and multi-level influences, some of which are amenable to change. Obesity prevention strategies should not only target individual behaviours but also the household environment and family practices. Although zBMI changes were modest, these findings are encouraging as small reductions can have population level impacts on childhood obesity levels.