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Climate change is a major threat to human welfare, biodiversity and ecosystem services. Climate change calls for changes in management of land and water resources. The coupling of and feedback from land use and land cover patterns in landscapes with ecosystem processes (nutrient cycling, water use, evaporation, heat and heat islands) and microclimate is known. Although information is inadequate from tropical land use practices such as intercropping, land rotation fallowing and agroforestry systems. However, understanding of the interactions of land cover patterns with ecosystem processes from cacao-based agroforestry landscapes may be useful in the development of strategies to advance adaptation and resilience to extreme weather shocks. Year round measurements were made of soil carbon contents and respiration, microbial biomass C, soil moisture and temperature regimes, soil organic matter pool, species specific carbon stocks, stand biomass, microclimatic-gradients in an agriculturally cultivated field and cacao-based agroforestry system of different ages. Our findings showed that land cover patterns and other elements in cultivated agricultural field and cacao-based agroforestry landscape modulated land surface-atmosphere fluxes and stocks of carbon, other biogeochemical cycles and microclimatic conditions. The results indicated that the high potentials of net gains in carbon (sources and sinks) from cacao-based agroforestry system is a promising CO2 mitigation strategy. Cacao-based agroforestry ecosystem contributes to terrestrial carbon budget (carbon stocks and fluxes), ameliorated weather conditions in addition to other ecological benefits and ecosystem health while the resultant enhanced carbon sequestration will reduce global warming. This information can be incorporated into existing strategies for addressing ecosystem (vegetation and soil) degradation and for agricultural, and forest land use plans in support of climate change adaptation and for rainforest ecosystem conservation.