Despite the substantial global investments in the COVID-19 research response, there were significant shortcomings in research funding allocation, demonstrated by fragmentation, funding of poor-quality studies and limited investments in research involving LMICs. To better understand the factors driving such shortcomings, I undertook “research-on-research”, with a focus on Africa. I first conducted a scoping review to assess research priority-setting activities and methodologies. This was followed by a mapping review of the UKCDR and GloPID-R COVID-19 Research Project Tracker to assess the alignment of funds allocated to global and regional research priorities. This was complemented by a qualitative study to explore the perspectives of researchers and grant managers, based in African research institutions, of factors influencing their access to funding for COVID-19 research. My findings revealed diverse methods applied in priority-setting activities during the COVID-19 pandemic. Moreover, reporting on these did not follow the reporting standards for health research priority-setting. I also found that while COVID-19 research in Africa aligned to global priorities, it failed to address region-specific research priorities. Multiple factors enabled or inhibited access to research funding in African institutions. Among the enablers were: supportive institutional remote work policies; supplementary funding to pre-existing grants; and expedited grant awarding processes. Institutional bureaucracy and unequal power among research partner institutions were barriers to accessing research funds. Several lessons for strengthening preparedness for future epidemics and pandemics in Africa emerged. These include: improving access to information across the system for financing health research; optimising existing funding models and creating new models for financing research in emergencies; strengthening research and grant management capacity in African research institutions; and, increasing local and regional financial commitments to health research. My findings highlight the complexities in health research funding processes, justifying the need for a holistic approach to implementing research funding policies for pandemic preparedness and response.