Abstract Background Overweight and obese children are likely to develop serious health problems. Among children in the U.S., Latino children are affected disproportionally by the obesity epidemic. Niños Sanos, Familia Sana (Healthy Children, Healthy Family) is a five-year, multi-faceted intervention study to decrease the rate of BMI growth in Mexican origin children in California’s Central Valley. This paper describes the methodology applied to develop and launch the study. Methods/Design Investigators use a community-based participatory research approach to develop a quasi-experimental intervention consisting of four main components including nutrition, physical activity, economic and art-community engagement. Each component’s definition, method of delivery, data collection and evaluation are described. Strategies to maintain engagement of the comparison community are reported as well. Discussion We present a study methodology for an obesity prevention intervention in communities with unique environmental conditions due to rural and isolated location, limited infrastructure capacity and limited resources. This combined with numerous cultural considerations and an unstable population with limited exposure to researcher expectations necessitates reassessment and adaptation of recruitment strategies, intervention delivery and data collection methods. Trial registration # NCT01900613. Trial registration NCT01900613.