Background The World Health Organization (WHO) defines health as a state of complete physical, mental, and social well-being and not merely the absence of disease or infirmity. Despite its importance, mental health provisions are often limited. In 2015, Indonesia had only 773 psychiatrists for 250 million residents. This shortage of specialist mental health professionals is shared by most Low- and Middle-Income Countries (LMICs) and is reflected in the Treatment Gaps in this region indicating the very small proportion of people who receive adequate mental health care for their needs. While the median worldwide Treatment Gap for psychosis is 32.2% (Kohn et al., 2004), in Indonesia it is more than 90%. Experts suggested integrating mental health care into primary care, to help bridge this gap (Mendenhall et al., 2014). The systematic introduction of the World Health Organization Mental Health Gap Action Programme into primary care clinics across Indonesia and the presence of a 15-year-old co-location of Clinical Psychologists in Yogyakarta province\u2019s primary care clinics presented an opportunity to assess the clinical and cost-effectiveness of both frameworks. Methods This research (\u201cthe trial\u201d) set out to develop an approach, and then implement it, to compare the adapted WHO mhGAP framework with the existing specialist framework within primary mental health services in Yogyakarta, Indonesia, through a pragmatic, two-arm cluster randomised controlled non-inferiority trial. This design enabled an examination of patients derived from whole populations in a \u2018real world\u2019 setting. The trial involved two phases: a pilot study in June 2016 with the objectives to refine data collection procedures and to serve as a practice run for clinicians involved in the trial; as well as a substantive trial beginning in December 2016. The 12-item General Health Questionnaire (GHQ-12) was established as a \u2018fairly accurate\u2019 screening tool using a Receiver Operating Curve study. Using the GHQ scoring method of 0-0-1-1, a threshold of 1\/2 was identified for use in clinical setting, i.e. the context of the trial. The primary outcome was the health and social functioning of participants as measured by the Health of the Nation Outcome Scale (HoNOS) and secondary outcomes were disability as measured by WHO Disability Assessment Schedule 2.0 (WHODAS 2.0), quality of life as measured by European Quality of Life Scale (EQ\u20105D-3L), and cost of intervention evaluated from a health services perspective, which aimed to determine the clinical effectiveness and cost-effectiveness of both frameworks at six months. Results During the recruitment period, 4944 adult primary care patients attended 27 participating primary care centres. Following screening (n=1484) and in-depth psychiatric interviews (n=394), 174 WHO mhGAP arm and 151 Specialist arm participants received a formal diagnosis and were recruited into the trial. The number of required participants per treatment arm, to provide statistical power of 0.80 and statistical bilateral significance value of 0.05 was estimated to be 96. A total of 153 participants of the WHO mhGAP arm and 141 of the Specialist arm were followed-up at six months, representing 90.8% of all participants diagnosed. At follow-up, 82% (n=126) participants of the WHO mhGAP arm indicated they had attended at least one treatment session during the trial, significantly more than in the Specialist Arm (69%; n=97), \uf0632 = 7.364, p=0.007. The WHO mhGAP arm was proven to be statistically not inferior to the Specialist arm in reducing symptoms of social and physical impairment, reducing disability, and improving health-related quality of life at six months. Cost-effectiveness analyses show that the Specialist arm was dominant for a unit of improvement in patient outcomes at six months. While the framework is more expensive for the Health System, participants in the Specialist arm were found to have larger improvements. Conclusion Given that both frameworks yielded positive patient outcomes, there is no immediate need to increase the absolute number of specialist mental health professionals in community psychiatry (i.e. replicate the specialist framework outside Yogyakarta). As most psychologists and psychiatrists in Indonesia reside in large cities, the current systematic roll-out of the adapted WHO mhGAP framework might address the need to strengthen non-stigmatising mental health care within community contexts, reflecting the preferences of primary care patients. In districts or provinces which could afford the additional cost, however, the Specialist framework was shown to be better at improving patient outcomes than the adapted WHO mhGAP framework. Existing resources for specialist care can be arranged in a hub-and-spoke (step-up care) model where higher-level interventions are provided for those with greater needs. The proposed model would free-up resources for advanced clinical training of the specialist workforce in key areas of need while keeping specialist services accessible. Trial Registration This trial has been registered with clinicaltrials.gov since 25 February 2016, NCT02700490. Ethical Standards Full ethics approval from the University of Cambridge, UK was received on 15 December 2015 (PRE.2015.108) and from Universitas Gadjah Mada, Indonesia on 14 April 2016 (1237\/SD\/PL.03.07\/IV\/2016). A condition of ethics approval from the University of Cambridge is that the investigator is covered by indemnity insurance and that participants are insured for the period of their participation. This was provided by the University of Cambridge Trial Insurance Office (609\/M\/C\/1510). Ethics approval from all the clusters was not required as each cluster (Puskesmas) is a local GP surgery which does not have its own ethics committee. Instead, approval to conduct research at the province of Yogyakarta including all five districts: Kota Yogyakarta, Sleman, Gunung Kidul, Kulon Progo, Bantul Districts was obtained from the Provincial Government Office (070\/REG\/V\/625\/5\/2016) following ethics approvals. Written consent to participate was obtained from clinicians taking part as well as all patient-participants.