Purpose The aim of the present study was to investigate the effect of the JUMP-in programme on sports participation, overall physical activity (PA), shuttle run score and body composition in 6–12-year-old children. Methods JUMP-in is a school-based strategy combining environmental policy, neighbourhood, parents- and personal components. A controlled trial was carried out in 19 primary schools including 2848 children (50% boys). Measures were performed at the beginning of the first school year (T0: 2006) and repeated at the end of the first (T1: 2007) and second school year (T2: 2008). Results A significant beneficial intervention effect was found on organised sports participation (OR 2.8 (2.2 to 3.6)). Effects were stronger for girls (OR 3.6 (2.3 to 5.6)), and for Moroccan (OR 4.2 (3.6 to 5.7)) and Turkish children (OR 3.2 (1.9 to 5.2)). Participation in organised sports was associated with increased shuttle run score. No significant intervention effects on overall daily PA rates and body composition were observed. Conclusion The present study proves that a school-based strategy combining environmental and personal interventions was successful in improving structural sports participation among children.