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Given the catastrophic decline in forest cover, the question of how to maintain forest biodiversity in managed “forest-like” land-use systems becomes a crucial question. This study focuses on the changes over time in forest structure and composition in two agroforestry systems subjected to continuous management. We selected, as our study sites, benzoin gardens in North Sumatra and rattan gardens in East Kalimantan, along with adjacent mature forests. In both study areas, we observed recovery patterns similar to those described in the literature for tropical forest succession, although these were not necessarily related to the time elapsed since the gardens were established. The structure and composition of the managed gardens are a compromise between two opposite forces. Firstly, the natural succession process increases basal area and plant species richness. Secondly, the intensity of human intervention reduces species richness and partially or totally impedes an increase in the basal area. The importance of those forces depends on the biological requirements of the species managed, which determine the intensity of human control. In benzoin gardens, subjected to highly intense management, the recovery process of the forest is exclusively related to the silvicultural activities carried out therein. In rattan gardens, with less intervention in the system, changes in structure and composition are partially related to succession.