The inclusion of shade trees into cocoa (Theobroma cacao L.) systems can generate livelihood opportunities for smallholder farmers. Yet, there is the need to examine the ecological context within which shade trees, and their functional traits, have a positive impact on ecosystem services in cocoa systems. Here, we used a network of farms of similar aged hybrid cocoa, in a nested design consisting of agroforestry or monoculture management, on three initial soil quality levels (poor, moderate or good) in two agroecological zones (humid or sub-humid) to investigate whether shade tree functional traits are linked with soil-based and cocoa-based ecosystem services. Initial soil quality level was the main driver of differences in soil organic matter, soil N, soil C:N, soil total C, soil permanganate-oxidizable C, while agroecological zone largely explained differences in cocoa yield and aboveground C. The inclusion of shade trees increased soil macrofauna abundance and mass but decreased cocoa aboveground C compared to cocoa monoculture plots. Importantly, within agroforestry systems, shade tree leaf traits expressed as community weighted means of SLA, leaf N, and leaf dry matter content explained differences in soil-based and cocoa-based ecosystem services. These results show that agroforestry systems have the potential to enhance soil-based ecosystem services without notably decreasing cocoa yield. And a trait-based approach to describe shade tree diversity can advance our understanding and management of shade tree-ecosystem service relationships in cocoa agroforestry systems.