Addressing the interconnected challenges of food security, climate change, and population growth requires innovative and adaptive approaches to sustainable agriculture. Agricultural best management practices (BMPs) provide a promising framework for enhancing resilience, improving resource efficiency, and promoting biodiversity. However, the effectiveness of BMPs’ implementation largely depends on their alignment with local environmental, social, and economic conditions. This study presents a novel methodology for selecting and implementing BMPs based on stakeholder preferences, ensuring solutions are contextually relevant and widely accepted. Developed within the European Commission-funded WATDEV project, this methodology integrates a bottom-up and top-down decision-making framework, incorporating the perspectives of farmers, policymakers, and experts. The approach has been tested in four East African countries: Kenya, Ethiopia, Sudan, and Egypt, demonstrating its adaptability across diverse agroecological settings. Through a structured assessment involving stakeholder engagement, data-driven BMP selection, and participatory decision support tools, the study identifies and prioritizes BMPs that optimize water use, soil conservation, and climate resilience. Findings highlight that community-driven BMP selection enhances adoption rates and ensures solutions are technically feasible, economically viable, and environmentally sustainable. The methodology provides a scalable blueprint for integrating stakeholder preferences into agricultural planning, offering valuable insights for policymakers, researchers, and practitioners working toward sustainable food systems in East Africa and beyond.