This article examines interactions between school-level and pupil-level measures of socio-economic status for pupil reports of the school environment and a range of risk behaviours and health outcomes. The baseline survey for the INCLUSIVE trial provided data on pupil affluence and pupil reports of the school environment, smoking, drinking, anti-social behaviour at school, quality of life and psychological wellbeing for over 6,000 pupils (aged 11-12 years) in 40 schools within a 1-hour train journey from central London. The level of socio-economic disadvantage of the school was measured using the percentage of pupils eligible for free school meals. Multilevel regression models examined the association between pupil affluence, the socio-economic composition of the school and the interaction between these with the school environment, risk behaviours and health outcomes. Our findings provide some evidence for interactions, suggesting that less affluent pupils reported lower psychological wellbeing and quality of life in schools with more socio-economically advantaged intakes. There appears to be a complex relationship for anti-social behaviour. Where pupil affluence and school socio-economic composition were discordant, pupils reported a higher number of anti-social behaviours. This article provides further evidence that less affluent pupils are more likely to engage in a variety of risk behaviours and experience worse health outcomes when they attend schools with more socio-economically advantaged intakes, supporting some of the mechanisms described in the theory of human functioning and school organisation.