With increasing access to antiretroviral therapy (ART) in South Africa, HIV has transitioned from a terminal illness to a long-term condition. It is likely to be accompanied by higher levels of disability and other chronic non-communicable diseases, resulting from the HIV itself, as well as adverse effects of medication. This requires an expansion of the purview of HIV care beyond direct HIV clinical care to also include a more comprehensive and integrated package of treatment and care for physical and mental conditions and their consequences. COBALT is a pragmatic cluster randomized controlled trial (RCT) in public sector primary care clinics in the North West Province of SA. It will assess mental health and HIV outcomes for depressed adults receiving ART by measuring the real-world effectiveness of a facility-based stepped care intervention combining depression case detection by non-physician clinicians with group counselling intervention delivered by lay-health workers.