BackgroundThe scale-up of antiretroviral treatment (ART) programmes has seen HIV/AIDS transition to a chronic condition characterised by high rates of comorbidity with tuberculosis, non-communicable diseases (NCDs) and mental health disorders. Depression is one such disorder that is associated with higher rates of non-adherence, progression to AIDS and greater mortality. Detection and treatment of comorbid depression is critical to achieve viral load suppression in more than 90% of those on ART and is in line with the recent 90-90-90 Joint United Nations Programme on HIV/AIDS (UNAIDS) targets. The CobALT trial aims to provide evidence on the effectiveness and cost-effectiveness of scalable interventions to reduce the treatment gap posed by the growing burden of depression among adults on lifelong ART.MethodsThe study design is a pragmatic, parallel group, stratified, cluster randomised trial in 40 clinics across two rural districts of the North West Province of South Africa. The unit of randomisation is the clinic, with outcomes measured among 2000 patients on ART who screen positive for depression using the Patient Health Questionnaire (PHQ-9). Control group clinics are implementing the South African Department of Health’s Integrated Clinical Services Management model, which aims to reduce fragmentation of care in the context of rising multimorbidity, and which includes training in the Primary Care 101 (PC101) guide covering communicable diseases, NCDs, women’s health and mental disorders. In intervention clinics, we supplemented this with training specifically in the mental health components of PC101 and clinical communications skills training to support nurse-led chronic care. We strengthened the referral pathways through the introduction of a clinic-based behavioural health counsellor equipped to provide manualised depression counselling (eight sessions, individual or group), as well as adherence counselling sessions (one session, individual). The co-primary patient outcomes are a reduction in PHQ-9 scores of at least 50% from baseline and viral load suppression rates measured at 6 and 12 months, respectively.DiscussionThe trial will provide real-world effectiveness of case detection and collaborative care for depression including facility-based counselling on the mental and physical outcomes for people on lifelong ART in resource-constrained settings.Trial registrationClinicalTrials.gov (NCT02407691) registered on 19 March 2015; Pan African Clinical Trials Registry (201504001078347) registered on 19/03/2015; South African National Clinical Trials Register (SANCTR) (DOH-27-0515-5048) NHREC number 4048 issued on 21/04/2015.Electronic supplementary materialThe online version of this article (10.1186/s13063-018-2517-7) contains supplementary material, which is available to authorized users.