The HEALTHY study was a multi-site randomized trial designed to determine whether a 3-year school-based intervention targeting nutrition and physical activity behaviors could effectively reduce risk factors associated with type 2 diabetes in middle school children. Pilot and formative studies were conducted to inform the development of the intervention components and the process evaluation methods for the main trial. During the main trial, both qualitative and quantitative assessments monitored the fidelity of the intervention and motivated modifications to improve intervention delivery. Structured observations of physical education classes, total school food environments, classroom-based educational modules, and communications and promotional campaigns provided verification that the intervention was delivered as intended. Interviews and focus groups yielded a multidimensional assessment of how the intervention was delivered and received, as well as identifying the barriers to and facilitators of the intervention across and within participating schools. Interim summaries of process evaluation data were presented to the study group as a means of ensuring standardization and quality of the intervention across the seven participating centers. Process evaluation methods and procedures documented the fidelity with which the HEALTHY study was implemented across 21 intervention schools and identified ways in which the intervention delivery might be enhanced throughout the study.