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Conservation systems involving trees enhance the sustainability of tropical soils. However, little is known on the effect of integrated systems with native and exotic trees on soil chemical quality in the eastern Amazon. We aimed to measure changes in soil chemical quality in integrated production systems in Pindaré-Mirim, Maranhão, Brazil. This study was carried out in 2017 and 2018, evaluating (i) perennial pasture; (ii) crop–livestock–forest integration-I (CLFI-I)—eucalyptus rows interspersed with maize + Urochloa brizantha intercropping; (iii) CLFI-II—babassu palm trees (Attalea speciosa Mart.) with maize + Megathyrsus maximus intercropping; and (iv) maize + M. maximus intercropping. Soil chemical attributes at depths of 0.00–0.10 m, 0.10–0.20 m, 0.20–0.30 m, and 0.30–0.50 m, forage productivity, and soil cover were evaluated. CLFI-II promoted the highest soil organic matter concentration in topsoil and highest pH, lowest Al3+ levels, and potential acidity (H+Al) at all soil depths. Soil under pasture showed the highest N, K+, Ca2+ concentrations, sum of bases, and cation exchange capacity. Changes in CLFI-II are associated with the babassu palm's ability to modulate the surrounding environment, giving the species a competitive advantage in anthropic environments. The time of adoption is crucial for improving soil fertility in the Brazilian eastern Amazon. Sustainable production systems in the region must comply with long-term management plans. [ABSTRACT FROM AUTHOR]