Agroforestry systems (AFS) are important agricultural land use in synergy with socio-environmental aspects, especially with cacao (Theobroma cacao L.) crop, a commodity mainly produced by smallholders in the humid tropics. In southern Para, Brazilian Amazon, farmers manage native shade trees growing with cacao, but species selection may be not appropriate to AFS maintenance over time. The objective of this study was to understand the shade trees transition between successional management phases of cacao-AFS, considering its initial shade (IS) and secondary shade (SS). It was sampled 10 plots in each situation (20,000m(2) in total) identifying individuals with CBH >= 15cm. As expected, floristic composition was different and SS had greater species richness and diversity than IS, where only 17% of species were the shared among them. Musa sp. and Carica papaya L. were found only in IS and were dominant species, representing almost a half of the individuals. Although there was increase of late succession species from IS to SS, this still keeps high abundance of early succession species, such as Cecropia sp. The result shows an unexploited potential products and gap of services provision, such as N-fixing. The conclusion highlights the necessity of long-term succession planning and management practices to guarantee cacao crop maintenance and improve diversification with other income sources, such as fruits and wood. The role of biodiversity conservation, provided by shade trees, should be the target of political strategies to encourage its maintenance, such as payment for ecosystems services or other economic incentives.