BACKGROUND: South Africa faces a complex dual burden of chronic communicable and non-communicable diseases (NCDs). In response, the Integrated Chronic Disease Management (ICDM) model was initiated in primary health care (PHC) facilities in 2011 to leverage the HIV/ART programme to scale-up services for NCDs, achieve optimal patient health outcomes and improve the quality of medical care. However, little is known about the quality of care in the ICDM model. The objectives of this study were to: i) assess patients' and operational managers' satisfaction with the dimensions of ICDM services; and ii) evaluate the quality of care in the ICDM model using Avedis Donabedian's theory of relationships between structure (resources), process (clinical activities) and outcome (desired result of healthcare) constructs as a measure of quality of care. METHODS: A cross-sectional study was conducted in 2013 in seven PHC facilities in the Bushbuckridge municipality of Mpumalanga Province, north-east South Africa - an area underpinned by a robust Health and Demographic Surveillance System (HDSS). The patient satisfaction questionnaire (PSQ-18), with measures reflecting structure/process/outcome (SPO) constructs, was adapted and administered to 435 chronic disease patients and the operational managers of all seven PHC facilities. The adapted questionnaire contained 17 dimensions of care, including eight dimensions identified as priority areas in the ICDM model - critical drugs, equipment, referral, defaulter tracing, prepacking of medicines, clinic appointments, waiting time, and coherence. A structural equation model was fit to operationalise Donabedian's theory, using unidirectional, mediation, and reciprocal pathways. RESULTS: The mediation pathway showed that the relationships between structure, process and outcome represented quality systems in the ICDM model. Structure correlated with process (0.40) and outcome (0.75). Given structure, process correlated with outcome (0.88). Of the 17 dimensions of care in the ICDM model, three structure (equipment, critical drugs, accessibility), three process (professionalism, friendliness and attendance to patients) and three outcome (competence, confidence and coherence) dimensions reflected their intended constructs. CONCLUSION: Of the priority dimensions, referrals, defaulter tracing, prepacking of medicines, appointments, and patient waiting time did not reflect their intended constructs. Donabedian's theoretical framework can be used to provide evidence of quality systems in the ICDM model.