Background: South Africa is experiencing colliding epidemics of HIV/AIDS and noncommunicable diseases. In response, the National Department of Health has implemented integrated chronic disease management aimed at strengthening primary health care (PHC) facilities to manage chronic illnesses. However, chronic care is still fragmented. This study explored how the health system functions to care for patients with comorbid type 2 diabetes (T2DM) and HIV/AIDS at a tertiary hospital in Soweto, South Africa. Methods: We employed ethnographic methods encompassing clinical observations and qualitative interviews with health care providers at the hospital (n=30). Data were transcribed verbatim and thematically analyzed using QSR NVivo 12 software. Findings: Health systemic challenges such as the lack of medication, untrained nurses, and a limited number of doctors at PHC clinics necessitated patient referrals to a tertiary hospital. At the hospital, patients with T2DM were managed first at the medical outpatient clinic before they were referred to a specialty clinic. Those with comorbidities attended different clinics at the hospital partly due to the structure of the tertiary hospital that offers specialized care. In addition, little to no collaboration occurred among health care providers due to poor communication, noncentralized patient information, and staff shortage. As a result, patients experienced disjointed care. Conclusion: PHC clinics in Soweto need to be strengthened by training nurses to diagnose and manage patients with T2DM and also by ensuring adequate medical supplies. We recommend that the medical outpatient clinic at a tertiary hospital should also be strengthened to offer integrated and collaborative care to patients with T2DM and other comorbidities. Addressing key systemic challenges such as staff shortages and noncentralized patient information will create a patient-centered as opposed to disease-specific approach to care.