Background The US HIV epidemic is driven by infections in men who have sex with men and characterized by profound disparities in HIV prevalence and outcomes for Black Americans. Black men who have sex with men living with HIV are reported to have worse care outcomes than other men who have sex with men, but the reasons for these health inequities are not clear. We planned a prospective observational cohort study to help understand the reasons for worse HIV care outcomes for Black versus White men who have sex with men in Atlanta. Objective The aim of this study is to identify individual, dyadic, network, neighborhood, and structural factors that explain disparities in HIV viral suppression between Black and White men who have sex with men living with HIV in Atlanta. Methods Black and White men who have sex with men living with HIV were enrolled in a prospective cohort study with in-person visits and viral suppression assessments at baseline, 12 months, and 24 months; additional surveys of care and risk behaviors at 3, 6, and 18 months; analysis of care received outside the study through public health reporting; and qualitative interviews for participants who experienced sentinel health events (eg, loss of viral suppression) during the study. The study is based on the Bronfenbrenner socioecological theoretical model. Results Men who have sex with men (n=400) were enrolled between June 2016 and June 2017 in Atlanta. Follow-up was completed in June 2019; final study retention was 80% at 24 months. Conclusions Health disparities for Black men who have sex with men are hypothesized to be driven by structural racism and barriers to care. Observational studies are important to document and quantify the specific factors within the socioecological framework that account for disparities in viral suppression. In the meantime, it is also critical to push for steps to improve access to care, including Medicaid expansion in Southern states, such as Georgia, which have not yet moved to expand Medicaid. International Registered Report Identifier (IRRID) DERR1-10.2196/21985