The WHO Regional Office for Africa (AFRO) COVID-19 Incident Management Support Team (IMST) was first established on 21 January 2020 to coordinate the response to the pandemic in line with the Emergency Response Framework and has undergone three modifications based on intra-action reviews (IAR). An IAR of the WHO AFRO COVID-19 IMST was conducted to document best practices, challenges, lessons learnt and areas for improvement from the start of 2021 to the end of the third wave in November 2021. In addition, it was designed to contribute to improving the response to COVID-19 in the Region. An IAR design as proposed by WHO, encompassing qualitative approaches to collecting critical data and information, was used. It employed mixed methods of data collection: document reviews, online surveys, focus group discussions and key informant interviews. A thematic analysis of the data focused on four thematic areas, namely operations of IMST, data and information management, human resource management and institutional framework/governance. Areas of good practice identified, included the provision of guidelines, protocols and technical expertise, resource mobilisation, logistics management, provision of regular updates, timely situation reporting, timely deployment and good coordination. Some challenges identified included a communication gap; inadequate emergency personnel; lack of scientific updates; and inadequate coordination with partners. The identified strong points/components are the pivot for informed decisions and actions for reinvigorating the future response coordination mechanism.