Abstract Background Important health benefits can be achieved when physical activity in children from low socio-economic status is promoted and sedentariness is limited. By specifying the mediating mechanisms of existing interventions one can improve future physical activity interventions. This study explored potential mediators of the long-term effect of the school-based multicomponent JUMP-in intervention on sport participation, outdoor play and screen time in Dutch primary schoolchildren from disadvantaged neighborhoods. Methods In total, 600 primary schoolchildren (aged 9.8 ± 0.7, 51% girls, 13% Dutch ethnicity, 35% overweight) from 9 intervention and 10 control schools were included in the analyses. JUMP-in was developed using Intervention Mapping, and targeted psychological and environmental determinants of physical activity. Outcome behaviors were self-reported sport participation, outdoor play, TV-viewing behavior and computer use. Potential mediators were self-reported psychological, social and physical environmental factors. Results JUMP-in was effective in improving sport participation after 20 months, but not in improving outdoor play, or reducing TV-viewing or computer time. JUMP-in was not effective in changing hypothesized mediators so no significant mediated effects could be identified. However, changes in self-efficacy, social support and habit strength were positively associated with changes in sport participation, and changes in social support, self-efficacy, perceived planning skills, enjoyment and habit strength were positively associated with changes in outdoor play. Changes in enjoyment was positively associated with changes in TV-viewing while parental rules were negatively associated. Having a computer in the bedroom and enjoyment were positively associated with changes in computer use, while changes in parental rules were negatively associated. Conclusions Besides a significant positive effect on sports participation, no significant intervention effect on outdoor play, screen time or ...