Gay, bisexual, and other men who have sex with men (MSM) are at high risk for human immunodeficiency virus (HIV) infection. In rights-constrained settings with pervasive stigma, peer outreach workers play a key role in recruitment and retention of MSM in HIV research, prevention, and treatment programs. We explored factors affecting the empowerment of peers in an HIV prevention and care study for MSM in Kisumu, Kenya, with the goal of improving program services and supporting good participatory practice. The Anza Mapema study, conducted from 8/2015-10/2017, aimed to enroll 700 MSM in a comprehensive package of find, test, link and retain in HIV prevention and care interventions, with quarterly follow-up over 12 months. Seventeen mostly heterosexual salaried staff implemented the clinical and research components of the study, while 13 gay and bisexual peers facilitated recruitment, retention, and participant education, supported by a monthly stipend. A community advisory board provided feedback on program methods and performance. In-depth interviews with peers and staff at two timepoints were used to obtain feedback and make program improvements. Thematic analysis was conducted, and results were presented to peers and staff for discussion and triangulation. Despite mutual appreciation of peers’ contributions to the project, peers and staff had different goals and vision for Anza Mapema. While staff focused on implementing the study protocol, peers envisioned broader programming including community-building activities, advocacy, mental health and substance use services, and economic empowerment. From the outset, power disparities and power struggles between peers and staff favored the staff, as peers were younger, less educated, and had lower compensation for their time. While peers appreciated the opportunity to help their community and the free health services provided by the project, they voiced concerns about stigmatizing attitudes from some staff, insufficient training, exclusion from decision-making, minimal representation on the study team, and lack of opportunities for advancement. Staff were supportive of peer’s requests but felt constrained by limited funding and rigid study timelines. Peers’ concerns were addressed at least in part through monthly team meetings with program leadership, weekly meetings with outreach coordinators, additional training, the promotion of one peer to a salaried position, and the development of community-building activities and a support group for participants who struggled with alcohol and drugs. Integration of gay and bisexual peers into HIV research and programming is critical in rights-constrained settings but challenged by disparities in power between peers and staff. Empowerment of peers is an important component of good participatory practice, and requires attention to training, inclusion in decision-making, opportunities for advancement, and support for community-building. Future studies that rely on peers for participant recruitment and retention should address these issues and make peer empowerment an overt component of the program.