Accumulation of heavy metals results in soil degradation and impairs the normal functioning of ecosystems. Thus, monitoring of heavy metals is essential in both pristine and polluted soils. Concentrations of heavy metals were determined in a pristine tropical agricultural soil using acid digestion procedures. The soil samples were also analyzed the physico-chemical parameters and biochar toxicity to earthworms. Data shows that the soil is acidic, with low organic matter content. The level of heavy metals ranged from <0.06 ± 0.0 – 595.8 ± 2.8 µg g−1. However, the concentrations were found to be below the soil regulatory standards of heavy metals in agricultural soils. Furthermore, increased addition of biochar to the soil caused toxic effect on earthworms over a 90 d biochar-soil contact time. The data provides baseline information of heavy metals in pristine agricultural soils from the region, and the effect of biochar amendments on tropical soils.