Background Prevention of overweight during early childhood seems promising. Objective To evaluate the effectiveness of the parenting-based BBOFT+ overweight prevention program on child BMI, child health behavior and parenting behavior among 0–36 month old children. BBOFT+ is an acronym for the key healthy lifestyle behaviors that are targeted in the BBOFT+ intervention: breastfeeding (B), daily breakfast (B), daily going outdoors (O), limiting sweet beverages (in Dutch, F) and minimal TV or computer time (T), complemented with healthy sleep behavior and improvement of parenting skills (+). Methods A cluster randomized controlled trial in newborn children visiting well-baby clinics, comparing the BBOFT+ intervention (N = 901) with care as usual (CAU) (N = 1094). In both groups, parents received regular well-child visits (±11 visits in the first 3 years). In the intervention group, care was supplemented with the BBOFT+ program, which focuses on improving parenting skills from birth onwards to increase healthy behavior. Questionnaires were filled in at child’s age 2–4 weeks, 6, 14 and 36 months. In multivariate analyses we corrected for child’s birthweight, age, ethnic background, mother’s educational level and BMI. Results No differences were found in weight status at 36 months between intervention and control group children. At 6 months, BBOFT+ parents reported their child drinking less sweet beverages than control parents (48% vs 54%;p = .027), and going outdoors daily with their child less often (57% vs 62%;p = .03). At 14 months, more BBOFT+ parents than control parents reported to have breastfed for six months or longer (32% vs 29%;p = .022). At 36 months, more BBOFT+ parents than control parents reported their child going outside daily (78% vs 72%;p = .011) and having less TV/computer time on week- (38% vs 46%;p = .001) and weekend days (48% vs 56%;p = .002). Also, BBOFT+ parents reported having more parental control than control parents (3.92 vs 3.89;p = .02). No significant differences were found for daily breakfast, sleep duration and parenting practices in adjusted analyses. Conclusion The BBOFT+ overweight prevention program showed small improvements in parent-reported child health behaviors, compared to care as usual; no effect was observed on child BMI. The identified modifiable elements are potentially relevant for interventions that aim to prevent overweight.