This paper explores farmers’ preferences and practices in relation to rice variety selection and management, and reports on a step-by-step experimentation with varieties in southern Guinea-Bissau. We used a mixed-methods and transdisciplinary approach from 2021–2023 to better understand why the poor uptake of formally introduced varieties persists despite a long track of research and interventions in the mangrove swamp rice (MSR) agroecosystem. We found that across the four villages studied, farmers possessed at least 18 varieties, but most households planted yearly only two to three varieties, mostly long-cycle ones. The MSR seed system was dominated by farm-saved seeds and farmers’ varieties. Farmers’ varieties and exogenous varieties acquired through informal channels were better adapted and yielded significantly more than varieties distributed by external actors. All tested varieties were equally affected by diverse socio-cultural, bio-physical, and environmental conditions and showed a wide range in grain yield (0–944 g/m2; mean 307 g/m2). Our findings demonstrate that poor infrastructure and poor understanding of farmers’ constraints, preferences, practices, and knowledge limit the impact of seed system interventions. We urge for research and development actors to adopt a transdisciplinary approach, especially when confronted with challenging realities and local ways of knowledge production in resource-constrained environments.