Background: As COVID-19 disease surges across much of the world, researchers in different settings have a unique opportunity to address the various research priorities that have been identified. The challenges that containment and mitigation strategies present for research, especially in resource limited settings, could be significant and negatively impact the essential contribution of these settings to COVID-19 research. Objectives: To describe experiences of conducting research during this pandemic, discuss challenges faced and present strategies implemented to address these challenges Methods: Malaria Consortium recently initiated an observational case series study to assess the magnitude and clinical consequences of co-infection of COVID-19, malaria, and other common infections. This study is being conducted in eight COVID-19 treatment centres in Uganda. Qualitative methods including observations and interviews were utilized to document experiences and mitigating strategies for identified challenges. The main outcomes were a descriptive narrative of experiences conducting this research, discussion of challenges faced, and presentation of strategies implemented to address these challenges. Results: Expedited ethical review and approval facilitated timely initiation of research activities. The primary clinical care teams at each treatment centre performed all study procedures to minimize infection. Given concerns about fomite transmission, considerations arose on how best to handle consent forms that had been signed or thumb-printed by patients to ensure that both hospital and research staff were not exposed to infection. Consenting severely ill or mentally impaired patients was also a challenge, especially when the next of kin was not available. Patient compensation was done through a mobile money/digital platform to avoid potential risks associated with cash. Patients, health care workers and study staff faced significant psychosocial challenges and anxiety that needed to be addressed. Conclusions: These experiences demonstrate that more adaptable and innovative approaches may be needed to support the implementation of research activities during this COVID-19 pandemic. This pandemic should also spur institutional review boards and investigators to respond to emerging challenges by updating policies and procedures around research review and approvals, and modifications in research methods.