School-based programs are widely implemented to combat childhood obesity, but these programs have mixed results. Dissemination and implementation science approaches to evaluation using qualitative methods can provide more robust details about program functioning that may be able to help explain the variation in the impact of these programs. Fourteen in-depth interviews were conducted with classroom teachers implementing a school-based program, the Integrated Nutrition Education Program (INEP), to explore their experience. Factors related to organization, individual and intervention levels emerged as facilitators and barriers to program implementation. Key factors were school culture at the organization level, individual perception and belief in the intervention at the individual level and program content, perceived complexity and adaptability at the intervention level. Socioeconomic status of the community and family involvement were contextual factors identified across all levels. Findings from this qualitative evaluation can be used for the quality improvement of INEP, but beyond this these can also be informative for other school-based programs to promote adoption, implementation and maintenance.