The integrated chronic disease management (ICDM) model was introduced as a response to the dual burden of HIV/AIDS and non-communicable diseases (NCDs) in South Africa, one of the first of such efforts by an African Ministry of Health. The aim of the ICDM model is to leverage HIV programme innovations to improve the quality of chronic disease care. There is a dearth of literature on the perspectives of healthcare providers and users on the quality of care in the novel ICDM model. This paper describes the viewpoints of operational managers and patients regarding quality of care in the ICDM model. In 2013, we conducted a case study of the seven PHC facilities in the rural Agincourt sub-district in northeast South Africa. Focus group discussions (n = 8) were used to obtain data from 56 purposively selected patients ≥18 years. In-depth interviews were conducted with operational managers of each facility and the sub-district health manager. Donabedian’s structure, process and outcome theory for service quality evaluation underpinned the conceptual framework in this study. Qualitative data were analysed, with MAXQDA 2 software, to identify 17 a priori dimensions of care and unanticipated themes that emerged during the analysis. The manager and patient narratives showed the inadequacies in structure (malfunctioning blood pressure machines and staff shortage); process (irregular prepacking of drugs); and outcome (long waiting times). There was discordance between managers and patients regarding reasons for long patient waiting time which managers attributed to staff shortage and missed appointments, while patients ascribed it to late arrival of managers to the clinics. Patients reported anti-hypertension drug stock-outs (structure); sub-optimal defaulter-tracing (process); rigid clinic appointment system (process). Emerging themes showed that patients reported HIV stigmatisation in the community due to defaulter-tracing activities of home-based carers, while managers reported treatment of chronic diseases by traditional healers and reduced facility-related HIV stigma because HIV and NCD patients attended the same clinic. Leveraging elements of HIV programmes for NCDs, specifically hypertension management, is yet to be achieved in the study setting in part because of malfunctioning blood pressure machines and anti-hypertension drug stock-outs. This has implications for the nationwide scale up of the ICDM model in South Africa and planning of an integrated chronic disease care in other low- and middle-income countries.