Integrating farmers’ preferences into the breeding and dissemination of new genotypes is a effective approach to enhance their successful adoption by farmers. In the case of sweet potato, a staple crop in many parts of West Africa, there is a need for more research on the selection criteria used by farmers when choosing which varieties to grow. This study aims to highlight farmers’ selection criteria for sweet potato varieties in the main production areas in Benin. A total of 480 farmers from the top three sweet potato production areas were surveyed. The relative importance of various traits for sweet potato farmers was evaluated using best-worst scaling methods. Latent class analysis was applied to find groups of farmers with similar preferences. Best-Worst Scaling analysis revealed that high root yield, root size, marketability, and early maturing were the most important variety selection criteria. Latent class analysis revealed three farmers’ groups referred to as ‘Yield potential’, ‘Market value’, and ‘Plant resilience’ classes. ‘Yield potential’ farmers were more likely to be from Atlantique and Alibori departments; they significantly committed more acreage to sweet potato production. The ‘Market value’ farmers highlighted the variety of root size and commercial value as the main selection criteria and consisted of farmers with primary education levels from the Ouémé department. ‘Plant resilience’ refers to a group of Alibori farmers who prioritize environmental issues and primarily grow sweet potatoes for self-consumption. Our findings shed light on farmers’ preferences and suggested that heterogeneity in sweet potato selection criteria was highly influenced by various socio-economic factors and location.