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Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.