The aim of the study was to determine the effects of a multi-component community-based health promotion intervention on body mass index (BMI) z-scores and waist circumference (WC) in three- to eight-year-old children. A quasi-experimental design was adopted to evaluate the effects of the SoL intervention involving three intervention and three control communities. The 19-month intervention was based on the supersetting approach and was designed to promote healthier eating and physical activity among children and their families. BMI z-scores and WC were measured at baseline and follow-up. At baseline, 238 (54%) and 214 (51%) of all eligible children were measured from intervention and control, respectively. The change over time in the BMI z-scores of children from the intervention group was significantly different from that of the control group (p = 0.001). BMI z-scores increased over time in the intervention group in contrast to the control group, whose BMI z-scores decreased (difference in change between groups 0.19 z-scores 95% CI 0.08, 0.30). No significant differences were observed for WC. The results showed no favourable effects of the intervention of Project SoL on BMI z-scores and WC in children. Further studies based on a larger sample size and a longer intervention duration are needed.