BACKGROUND: Adolescents in Latin America are at high risk for unwanted and unplanned pregnancies, which often result in unsafe abortions or poor maternal health outcomes. Both young men and women in the region face an increased risk of sexually transmitted infections due to inadequate sexual and reproductive health information, services and counselling. To date, many adolescent health programmes have targeted a single determinant of sexual and reproductive health. However, recent evidence suggests that the complexity of sexual and reproductive health issues demands an equally multi-layered and comprehensive approach. METHODS: This article describes the development, implementation and evaluation design of the community-embedded reproductive health care for adolescents (CERCA) study in three Latin American cities: Cochabamba (Bolivia), Cuenca (Ecuador) and Managua (Nicaragua). Project CERCA's research methodology builds on existing methodological frameworks, namely: action research, community based participatory research and intervention-mapping.The interventions in each country address distinct target groups (adolescents, parents, local authorities and health providers) and seek improvement of the following sexual health behaviours: communication about sexuality, sexual and reproductive health information-seeking, access to sexual and reproductive health care and safe sexual relationships.In Managua, we implemented a randomised controlled study, and in Cochabamba and Cuenca we adopted a non-randomised controlled study to evaluate the effectiveness of Project CERCA interventions, in addition to a process evaluation. DISCUSSION: This research will result in a methodological framework that will contribute to the improved design and implementation of future adolescent sexual and reproductive health interventions. TRIAL REGISTRATION: ClinicalTrials.gov (NCT01722084).