Lebanon is one of the most unequal countries in the world, whose economy, social welfare and public health system struggle to meet the needs of the Lebanese and over one million Syrian refugees. Researchers applied Community Based Participatory Research (CBPR) methodology in collaboration with a non-governmental organization (NGO) in an underserved Beirut neighborhood from 2014 through 2016, aiming to address health inequities, build social cohesion among refugees and host populations, and empower community members to develop a community health intervention. We recruited a community advisory board (CAB), conducted six focus groups and sixteen individual interviews, and held several community meetings. In response to the study findings, NGO staff, researchers and community members agreed to work together on a trash collection initiative as a community health intervention. Ultimately, we found the CBPR toolkit to be insufficient to the empirical reality: a series of structural challenges due to entrenched local and national hierarchies, ineffective political processes, and inter- and intra-group conflict driven by competition over privatized social services. Together these resulted in a lack of trust in the collaborative process wherein study participants solicited researchers for aid in return for their involvement, mirroring the Lebanese patronage system. Ultimately, the most expedient path toward change was not through empowerment of oppressed community participants, but through the action of already powerful local individuals. In conclusion, structural inequalities limit the participatory and emancipatory possibilities of CBPR research. Power mapping exercises, which are often used in community organizing, offer an important opportunity to assess viability and lay the groundwork for CBPR projects. Academic and popular media in the Middle East often focus on religious, sectarian conflict; however, in our study conflict both between and among social groups was driven by competition over material resources more than cultural or religious differences.