The degree to which the maintenance of carbon (C) stocks and tree diversity can be jointly achieved in production landscapes is debated. C stocks in forests are decreased by logging before tree diversity is affected, while C stocks in monoculture tree plantations increase, but diversity does not. Agroforestry can break this hysteresis pattern, relevant for policies in search of synergy. We compared total C stocks and tree diversity among degraded forest, complex cacao/fruit tree agroforests, simple shade-tree cacao agroforestry, monoculture cacao, and annual crops in the Konawe District, Southeast Sulawesi, Indonesia. We evaluated farmer tree preferences and the utility value of the system for 40 farmers (male and female). The highest tree diversity (Shannon–Wiener H index 2.36) and C stocks (282 Mg C ha−1) were found in degraded forest, followed by cacao-based agroforestry systems (H index ranged from 0.58–0.93 with C stocks of 75–89 Mg ha−1). Male farmers selected timber and fruit tree species with economic benefits as shade trees, while female farmers preferred production for household needs (fruit trees and vegetables). Carbon stocks and tree diversity were positively related (R2 = 0.72). Adding data from across Indonesia (n = 102), agroforestry systems had an intermediate position between forest decline and reforestation responses. Maintaining agroforestry in the landscape allows aboveground C stocks up to 50 Mg ha−1 and reduces biodiversity loss. Agroforestry facilitates climate change mitigation and biodiversity goals to be addressed simultaneously in sustainable production landscapes.

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Alternating degradation and restoration phases of soil quality, as is common in crop-fallow systems, can be avoided if the restorative elements of trees and forests can be integrated into productive agroforestry systems. However, evidence for the hypothesis of ‘internal restoration’ in agroforestry is patchy and the effectiveness may depend on local context. We investigated to what extent cocoa (Theobroma cacao, L.) agroforestry can recover soil structure and infiltration in comparison to monoculture systems across the Konaweha Watershed, Southeast Sulawesi. We compared soil organic carbon, fine root length and weight, soil aggregate stability, macroporosity and infiltration from three soil layers at five land use systems: i.e. degraded forests, 9–14 years old of complex-cocoa agroforestry, simple-cocoa agroforestry, monoculture cocoa and 1–4 years old annual food crops, all with three replications. In general, roots were concentrated in the upper 40 cm of soil depth, contained of 70% and 86% of total fine root length and weight. Compared to simple agroforestry and cocoa monoculture, complex agroforestry had greater root length and weight in the topsoil, even though it attained only half the values found in degraded forests. Higher root density was positively correlated to soil organic carbon. In upper soil layers, complex agroforestry had slightly higher soil aggregate stability compared to other agricultural systems. However, no significant difference was found in deeper layers. Complex agroforestry had higher soil macroporosity than other agricultural systems, but not sufficient to mimic forests. Degraded forests had two times faster steady-state soil infiltration than agricultural systems tested (13.2 cm h−1 and 6 cm h−1, respectively), relevant during peak rainfall events. Compared to other agricultural systems, complex agroforestry improves soil structure of degraded soil resulting from forest conversion. However, a considerable gap remains with forest soil conditions.