Interventions to promote physical activity are important in preventing children from becoming overweight. Many projects have been developed but only a few showed (moderate) effects. JUMP-in is a systematically developed primary-school-based intervention that focuses on the use of theory, environmental changes, parental influences and cooperation with multi-level parties in intervention development. The effects of JUMP-in were evaluated with a quasi-experimental pre-test/post-test research design. In total, 510 children from Grades 4, 5 and 6 of four intervention schools and two control schools in Amsterdam were followed for an intervention period of one school year. Changes in physical activity as well as in the social cognitive determinants were assessed using self-reports. In addition, a process evaluation has been executed. The results show that JUMP-in was effective in influencing physical activity, especially among children from Grade 6. Children in the control group decreased their level of physical activity considerably, while activity levels in intervention children from Grade 6 remained stable. The intervention effects could not be explained by changes in the measured social cognitive determinants. In contrast, process information illuminated differences in intervention effects between the participating schools. The results from the JUMP-in study show the importance of intervention designs that focus on a theory-based mix of relevant environmental and social cognitive factors.