BACKGROUND: For a decade, experts have suggested integrating mental health care into primary care to help bridge mental health Treatment Gap. General Practitioners (GPs) are the first port-of-call for many patients with mental ill-health. In Indonesia, the WHO mhGAP is being systematically introduced to its network of 10,000 primary care clinics as an add-on mental health training for pairs of GPs and Nurses, since the end of 2015. In one of 34 provinces, there exists an integrated care model: the co-location of clinical psychologists in primary care clinics. This trial evaluates patient outcomes among those provided mental health care by GPs with those treated by clinical psychologists in primary care. METHODS: In this partially-randomised, pragmatic, two-arm cluster non-inferiority trial, 14 primary care clinics were assigned to receive the WHO mhGAP training and 14 clinics with the co-location framework were assigned to the Specialist arm. Participants (patients) were blinded to the existence of the other pathway, and outcome assessors were blinded to group assignment. All adult primary care patients who screened positive for psychiatric morbidity were eligible. GPs offered psychosocial and/or pharmacological interventions and Clinical Psychologists offered psychosocial interventions. The primary outcome was health and social functioning as measured by the HoNOS and secondary outcomes include disability measured by WHODAS 2.0, health-related quality of life measured by EQ-5D-3L, and resource use and costs evaluated from a health services perspective, at six months. RESULTS: 153 patients completed the outcome assessment following GP care alongside 141 patients following Clinical Psychologists care. Outcomes of GP care were proven to be statistically not inferior to Clinical Psychologists in reducing symptoms of social and physical impairment, reducing disability, and improving health-related quality of life at six months. Economic analyses indicate lower costs and better outcomes in the Specialist arm and suggest a 50% probability of WHO mhGAP framework being cost-effective at the Indonesian willingness to pay threshold per QALY. CONCLUSION: General Practitioners supported by nurses in primary care clinics could effectively manage mild to moderate mental health issues commonly found among primary care patients. They provide non-stigmatising mental health care within community context, helping to reduce the mental health Treatment Gap. TRIAL REGISTRATION: ClinicalTrials.gov NCT02700490.