Comprehensive sexuality education (CSE) aims to prepare adolescents for safe, healthy, and fulfilling lives. The aim of this study was to assess the perspective of key informants regarding CSE content to prevent teenage pregnancy, as well as to identify implementation barriers in predominantly indigenous communities in Chiapas, Mexico. We conducted a descriptive qualitative study using semi-structured interviews to explore three different groups' perceptions, opinions and experiences. Adhering to grounded theory principles, we performed an inductive analysis and identified categories of interest. A total of 45 key informants (16 school staff members, 15 health personnel and 14 community leaders) were interviewed. School staff members are primarily responsible for CSE. Among all the participants, we identified a lack of training and the presence of prejudices. The information provided to adolescents by the informants was diverse and at times, incomplete. There was limited parental involvement and even opposition to sharing CSE content. Deeply rooted customs and traditions within a patriarchal context posed a significant obstacle to the implementation of CSE in the studied communities. Gaining a deeper understanding of rural and Indigenous contexts can facilitate the identification of barriers and promote the design of targeted strategies to reduce obstacles to pregnancy prevention in vulnerable populations.