The conversion of natural ecosystem to pasture or agricultural fields is the main factor of soil fertility and aboveground biomass decline in the Amazon basin. Our aim here was to present the impacts on soil chemical properties and aboveground biomass associated with four land covers (Coffea canephora, natural ecosystem, pasture and Theobroma cacao) from the Amazon basin, Amazonas, Brazil. The soil pH, soil organic carbon (SOC), SOC stock, phosphorus (P), Ca2+, Al3+, H++Al3+, sum of bases, cation exchange capacity (CEC), base saturation and aluminium saturation varied among the studied land covers. We observed a decrease in SOC stock by 82.9%, 33.1% and 79.5% when comparing the results of C. canephora, pasture and T. cacao with the natural ecosystem.Principal component analysis (PCA) showed that bulk density, soil pH, base saturation, Ca2+, K+, aboveground biomass increment (ABI), SOC stock, Al3+ and aluminium saturation were the main factors contributing to 86.45% of the data variance. Additionally, the proposed predictive models indicated that: (i) ABI was strongly influenced by soil pH, SOCstock, K+, Ca2+, base saturation and bulk density and (ii) SOCstock was strongly influenced by K+, Ca2+ and Al3+. The results of our study highlighted the importance of considering the conversion of natural ecosystems, aiming to find more suitable systems (e.g., agroforestry systems) in Brazil's Legal Amazon, based on the sustainable ways that simulate similar conditions to that occuring in the soil of natural ecosystems, since even the studied monocropping systems (T. cacao and C. canephora) that aimed to recover land degradation showed lower ABI and SOC stocks. Thus, future studies must consider the use of agroforestry systems with these crops to exploit positive results among soil chemical properties and aboveground biomass increment.