BACKGROUND: This study assessed the effects of the “Jump-in” whole-school intervention in Amsterdam, the Netherlands, on children's weight development by comparing children exposed to the intervention and controls from 3 other large Dutch cities. Jump-in is a comprehensive intervention that aims to stimulate healthy nutrition and physical activity in children at primary schools in Amsterdam. In addition, the relationship between the intervention's implementation degree and its effectiveness was studied. METHODS: Demographic and anthropometric data, collected by youth health care professionals via routine health checks at T0 (2014) and T1 (2019), were used to analyze possible intervention effects by comparing the weight development of children exposed to the Jump-in intervention versus unexposed controls. Implementation logs from health promotion professionals were used to determine intervention effects per implementation degree. Multilevel regression analyses were used for all analyses. RESULTS: In total, 4299 children were included mean age ± 5.5 years (T0), 10.6 years (T1), and ≈50% boys/girls at both times. Receiving the fully implemented intervention resulted in a decline in standardized body-mass index (zBMI) compared to the controls (−0.23, confidence interval [CI] −0.33, −0.13). It also led to higher odds to move into a healthier weight category over time (odds ratio [OR] 1.36, CI 1.06, 1.74), yet no statistically significant shift towards a healthy weight was found. CONCLUSIONS: Relative to the controls, children exposed to the intervention showed positive zBMI developments, with stronger effects when the implementation degree was higher. Despite positive results, creating more impact might require the further integration of school-based programs into whole-systems approaches that include other energy-balance behaviors.