External Quality Assessment (EQA) surveys performed by the World Health Organization Regional Office for Africa (WHO AFRO) revealed the need for the strengthening of public health microbiology laboratories, particularly for testing of epidemic-prone diseases in the African Region. These surveys revealed common issues such as supply chain management, skilled personnel, logistical support and overall lack of quality standards. For sustainable improvements to health systems as well as global health security, deficiencies identified need to be actively corrected through robust quality assurance programmes and implementation of laboratory quality management systems. Given all the pathogens of public health importance, an external quality assessment programme with a focus on vaccine-preventable diseases and emerging and re-emerging dangerous pathogens is important, and should not be stand-alone, but integrated within laboratory networks as seen in polio, measles, yellow fever and rubella. In 2015, WHO AFRO collaborated with the US Centers for Disease Control and Prevention, the London School of Hygiene & Tropical Medicine and partners in a series of consultations with countries and national and regional EQA providers for the development of quality assurance models to support HIV point-of-care testing and monitoring. These consultations revealed similar challenges as seen in the WHO AFRO surveys. WHO AFRO brought forth its experience in implementing quality standards for health programmes, and also opened discussions on how lessons learned through such established programmes can be utilised to supporting and strengthening the introduction of early infant diagnosis of HIV and viral load point-of-care testing. An optimised external quality assessment programme will impact the ability of countries to meet core capacities, providing improved quality management systems, improving the confidence of diagnostic network services in Africa, and including capacities to detect events of international public health importance.