In sub-Saharan Africa, rice production from smallholder farms remains extremely low due to limited fertilizer inputs and nutrient-deficient soils. Therefore, improving nutrient-use efficiency is a critical challenge for increasing rice yield in the region. In the project entitled “Breakthrough in Nutrient Use Efficiency for Rice by Genetic Improvement and Fertility Sensing Techniques in Africa,” we aimed to overcome this challenge by developing new varieties with the Pup1 locus, which enhances root development; promoting the P-dipping technique, which refers to the localized phosphorus application to seedling roots at transplanting; and utilizing rapid soil diagnosis methodologies to enable selective fertilizer applications. Furthermore, socioeconomic assessments have revealed that increasing rice yields improves farmers’ cash revenue and nutritional status, particularly in terms of energy and micronutrients, by accelerating the purchase of nutritious food items (vegetables, fruits, and meat/fish) in Madagascar. The research output was disseminated to thousands of local farmers to help address food security issues in Madagascar. This study provides a practical example of a transdisciplinary approach for delivering research outputs to beneficiaries by involving researchers, policymakers, extension officers, and private entities, such as fertilizer dealers and seed producers.