Background Building community capacity in secondary schools is a promising strategy for the sustainable implementation of school-based health promotion. The Fit Lifestyle at School and at Home (FLASH) intervention explored how building community capacity works for the prevention of overweight following four strategies: leadership, participatory school culture, tailored health-promotion activities, and local networks. This study evaluates the intervention's impact on community capacity and capacity-building processes over a period of 3 years, as well as its effects on adolescents' BMI and waist circumference. Methods A mixed-methods design guided by the RE-AIM framework was used. Impact on community capacity was evaluated with semi-structured interviews at the start and end of the intervention and analyzed using an anchored coding scale. Capacity-building processes were evaluated using interviews, journals, questionnaires, and the minutes of meetings. The effects on BMI z-scores and waist circumference were evaluated using a quasi-experimental design comparing an intervention (IG) and reference group (RG), based on multi-level analyses. Results Community capacity improved across all intervention schools but varied between capacity-building strategies. Leadership recorded the greatest improvements, aided by the appointment of Healthy School Coordinators, who increasingly focused on coordinating processes and fostering collaborations. Participatory school culture also improved through the adoption and implementation of participatory methods and a general increase in awareness concerning the importance of the Healthy School approach. Although additional health-promotion activities were implemented, stakeholders struggled with tailoring these to the specific dynamics of their schools. Limited improvements were observed in setting-up local networks that could help schools encourage healthy behavior among pupils. Differences in BMI z-scores between IG and RG over the total sample were negligible whereas waist ...