Soil degradation, driven by natural and anthropogenic factors, threatens our ability to support the growing global population and their well-being. Land use systems (LUS) that serve as an interface between 'actors' and 'land cover' can be characterized by GxExM interplay, representing the Genotype (G) by Environment (E) interactions, subject to Management (M). GxExM is a major cause of soil degradation. However, GxExM interactions can also serve as the basis for soil restoration, such as through agroforestry practices that involve retaining, planting, and wellmanaging (M) the right trees (G) in the right places on farms (E). This thesis investigates the capacity of cacao and coffee-based agroforestry systems in Indonesia to support soil recovery from various disturbances while maintaining their multifunctionality and economic performance. To address this question, a comprehensive approach involving spatial patterns, dynamic processes, and modeling techniques was applied. The thesis started with a focus on the soil recovery of different LUS following deforestation in Southeast Sulawesi, Indonesia. The study compared various LUS, including remnant forest, cacao-based agroforestry systems (simple and complex), cacao monoculture, and annual food crops. The findings revealed that complex agroforestry systems with diverse tree species exhibited higher root density in the upper soil layer, which was positively correlated with soil organic carbon (SOC). The increases in root density and SOC were associated with improved macroporosity, although the impact on aggregate stability and soil infiltration was modest. Furthermore, the thesis explores the multifunctionality and economic performance of cacao-based agroforestry systems using the process-based WaNuLCAS model. Different agroforestry systems involving the companion trees and crops were evaluated against various scenarios, including cacao root densities, soil textures, and climate regimes. The simulation results indicated that cacao agroforestry systems outperformed monoculture in terms of carbon stocks but had limited effects on water-related functions. Additionally, high root density cacao systems demonstrated better resilience to water scarcity, emphasizing the importance of root structure. Integration of cacao with annual crops or fruit trees showed the highest economic performance, with fruit tree combinations being more labor-efficient. However, intercropping cacao with fastgrowing trees in water-limited regions was detrimental to multifunctionality and economic performance. The next part of the thesis investigates the impact of volcanic ash deposition on topsoil properties and their recovery in different LUS around Mt. Kelud in East Java, Indonesia. The study compared soil properties before and after the volcanic eruption in remnant forest, coffee-based agroforestry (simple and complex), and annual food crops. Within three years, volcanic ash homogenized soil properties, affecting litter thickness, aggregate stability, and soil infiltration. Although these prope...