Strengthening research capacity in low-and-middle-income countries is essential to drive socioeconomic development and to achieve the Sustainable Development Goals. Understanding strengths and weaknesses in institutions' research capacity can guide effective targeting of investments and resources. This study assessed the capacity of institutions undertaking research in natural science topics in Africa to identify priority capacity gaps for future investment.Assessments were conducted in eight African institutions that were partners in a UK-Africa programme to strengthen research capacity in renewable energy, soil-related science, and water and sanitation. Assessments involved eighty-six interviews and three focus group discussions to identify institutions' research capacity strengths and gaps against an evidence-informed benchmark. Use of the same interview guides and data collection processes across all institutions meant that findings could be compared.Common research capacity gaps were: lack of, or poorly maintained, equipment; unreliable, slow procurement systems; insufficient opportunities for developing the skills of research support staff such as administrators and technicians; dysfunctional institutional email communication systems; insufficient focus on the development of 'soft' researcher skills such as ethics, academic writing and, in non-Anglophone countries, English language. Programme strengths were the South-South and South-North partnerships for sharing and cascading expertise and resources, joint writing of proposals and publications, and improved individual and institutional visibility.There were many similarities in research capacity gaps irrespective of the institutions' natural sciences research focus, and these were similar to those reported in the health sector. Common capacity needs are improving the skills of technicians and administrators to support research activities, soft skills training for researchers, and more effective pan-institutional e-communication systems. These could be strategic investment targets for the joint efforts of national governments and international organisations that fund programmes for strengthening research capacity in low- and middle-income countries.