BACKGROUND: The Good School Toolkit, a complex behavioural intervention designed by Raising Voices a Ugandan NGO, reduced past week physical violence from school staff to primary students by an average of 42% in a recent randomised controlled trial. This process evaluation quantitatively examines what was implemented across the twenty-one intervention schools, variations in school prevalence of violence after the intervention, factors that influence exposure to the intervention and factors associated with students' experience of physical violence from staff at study endline. METHODS: Implementation measures were captured prospectively in the twenty-one intervention schools over four school terms from 2012 to 2014 and Toolkit exposure captured in the student (n = 1921) and staff (n = 286) endline cross-sectional surveys in 2014. Implementation measures and the prevalence of violence are summarised across schools and are assessed for correlation using Spearman's Rank Correlation Coefficient. Regression models are used to explore individual factors associated with Toolkit exposure and with physical violence at endline. RESULTS: School prevalence of past week physical violence from staff against students ranged from 7% to 65% across schools at endline. Schools with higher mean levels of teacher Toolkit exposure had larger decreases in violence during the study. Students in schools categorised as implementing a 'low' number of program school-led activities reported less exposure to the Toolkit. Higher student Toolkit exposure was associated with decreased odds of experiencing physical violence from staff (OR: 0.76, 95%CI: 0.67-0.86, p-value< 0.001). Girls, students reporting poorer mental health and students in a lower grade were less exposed to the toolkit. After the intervention, and when adjusting for individual Toolkit exposure, some students remained at increased risk of experiencing violence from staff, including, girls, students reporting poorer mental health, students who experienced other violence and those reporting difficulty with self-care. CONCLUSIONS: Our results suggest that increasing students and teachers exposure to the Good School Toolkit within schools has the potential to bring about further reductions in violence. Effectiveness of the Toolkit may be increased by further targeting and supporting teachers' engagement with girls and students with mental health difficulties. TRIAL REGISTRATION: The trial is registered at clinicaltrials.gov , NCT01678846, August 24th 2012.