The COVID-19 pandemic spread rapidly in South Africa since 5 March 2020. Reliable, accurate and timely data (laboratory, epidemiological and clinical) were needed for data-driven, evidence-based informed decision-making to guide response, planning, containment, and mitigation. We describe data management systems during the COVID-19 pandemic in South Africa, focusing on data sources, analysis, dissemination, lessons learnt and recommendations made/implemented.