Globally, the Coronavirus (COVID-19) pandemic caused disruptions in socio-economic activities. It did not spare higher education institutions, and the research culture was the most affected area. Compared to industrialised countries, relatively little research has been conducted in West Africa on the impacts of COVID-19, especially considering research ecosystems and researchers. This motivated the present study, which explores how the pandemic affected African research culture from a gendered perspective. Specifically, this study focuses on two universities in West Africa: University of Cape Coast in Ghana and Université Félix Houphouët-Boigny in Côte d'Ivoire. Using data collected in these two universities, we examined the gender-specific impacts of COVID-19 on research culture in these institutions. The pandemic negatively affected time allocation to research, research funding and output, academic mobility, and career ambitions of researchers. The effects of the pandemic have been differently experienced by male and female researchers, particularly in terms of time allocation to research, research funding and career ambitions. Based on our findings, we recommend that West African higher education decision-makers increase budgetary allocations for research and implement targeted incentives to promote gender equality in academia. Additionally, we recommend that African HEIs develop and implement policies that foster an inclusive research culture.