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The dominance of a few staple crops (maize, rice, and wheat) in most agricultural systems hampers the application of interventions to improve food security and nutrition. Research and development attention has focused on improving the production and utilization of these crops, leaving other crops under‐researched and underutilized. Subsequently, there have been high malnutrition rates due to poor diet diversity, yet there are "opportunity crops" that remain under researched. The opportunity crops can unlock solutions to food insecurity, malnutrition, a lack of biodiversity, and indeed poor climate adaptation. The study explored diversification in agricultural systems to analyze whether reorientation of research investment to include under‐researched crops can increase nutrient gain and enhance dietary diversity. Research outputs benchmarked as the number of publications from three leading African universities, Nairobi, Pretoria, and Ghana, were related to crop diversity and nutrition of crops in five clusters: cereals, vegetables, legumes, roots and tubers, and nuts. The findings show that maize was the predominantly researched crop across the three institutions. Low research outputs were observed for pearl millet, finger millet, and yam across the three institutions: amaranth and nightshade (Pretoria), sweet potatoes (Pretoria and Ghana), Marama bean (Nairobi), and soya bean (Nairobi and Ghana). There was nutrient gain across all five clusters, particularly from under‐researched indigenous crops such as finger millet, amaranth, nightshade, yam, sweet potatoes, Marama bean, and soybean. Nutrient gain was contributed more by cereals and root and tuber crops from Pretoria, vegetables and nuts (Ghana), as well as legumes (Nairobi). The findings demonstrate that incorporating research on the least researched crops with successful integration of other research and development initiatives (policy and dissemination) can increase nutrition and improve dietary diversity. The nutrient gain will positively affect food security and nutrition, contributing to the achievement of Africa Agenda 2063, the United Nation's Sustainable Development Goals, and reducing food imports. The findings can inform research investment and decision across different institutions within the African continent. Research investment targeting crops such as finger millet, amaranthus, sweet potatoes, soya beans, and cashew nuts is needed considering the nutritional contribution, climate change adaptability, market potential, and biodiversity contribution. Further analysis should explore production, socio‐economic (marketability and income generation), and environmental gains (adaptive ability to climate change) for specific crops. The development of frameworks to guide the analysis of the nature and scope of factors affecting the contribution of these crops to food security and nutrition, as well as research on specific crops considering geographic distribution and institutional involvement, is also needed. [ABSTRACT FROM AUTHOR]