Provision of high-quality HIV care is challenging, especially in rural primary care clinics in high HIV burden settings. We aimed to better understand the main challenges to quality HIV care provision and retention in antiretroviral treatment (ART) programs in rural South Africa from the health care providers' perspective. We conducted semi-structured qualitative interviews with 23 providers from nine rural clinics. Using thematic and framework analysis, we found that providers and patients face a set of complex and intertwined barriers at the structural, programmatic, and individual levels. More specifically, analyses revealed that their challenges are primarily structural (i.e., health system- and microeconomic context-specific) and programmatic (i.e., clinic- and provider-specific) in nature. We highlight the linkages that providers draw between the challenges they face, the motivation to do their job, the quality of the care they provide, and patients' dissatisfaction with the care they receive, all potentially resulting in poor retention in care.