Agroecological approaches promoting healthy and sustainable production cannot succeed without the buy-in of producers. In terms of agroforestry, particularly cocoa-based agroforestry, several models exist in Côte d’Ivoire. These include traditional agroforestry systems that have been identified in several regions, including central Côte d’Ivoire. The motivation of producers in the centre to adopt and sustain these agroforestry systems remains strong despite the low yields observed compared to the national average. This study was conducted to understand how farmers’ perceptions of associated trees influence the sustainability of traditional cocoa agroforestry systems. It set out to analyse producers’ perceptions of trees, given that their empirical knowledge and cultural perceptions play a key role in the conservation of trees that contribute to the resilience, diversification of uses, and sustainability of cocoa-based agroforestry systems. To this end, ethnobotanical surveys were conducted among 102 producers in the Kokumbo sub-prefecture (central Côte d’Ivoire). These surveys were supplemented by floristic and phyto-ecological data collected on the respondents’ plantations. Descriptive and textual analyses of the data collected show that trees are considered an integral part of cocoa plantations. They enable cocoa trees to withstand the long dry season imposed by the climate in this area. The plantation also provides various ecosystem services, as the associated woody species are selected for their beneficial contribution to the cocoa tree and/or the producer. This is the case with Ricinodendron heudelotii, a multifunctional tree that, in addition to being used in medicine and as a condiment, is beneficial to cocoa trees. However, the challenges faced by rural households are prompting some producers to turn away from the values they have been taught and increasingly move towards less sustainable full-sun production systems, thereby threatening the local climate balance and the food security of rural households.