Palm oil production in Southeast Asia often occurs on nutrient-poor, acidic soils converted from primary forest. Both the agricultural conversion and the production of oil palm are subsidised in Indonesia. As well as depleting soil organic C and plant nutrients, agricultural production on these soils can result in the accumulation of trace elements (TEs)—including micronutrients and non-essential trace elements—from the use of TE-containing agrichemicals including phosphate fertilisers and Cu fungicides. We tested the hypothesis that palm soils will have lower C concentrations than forest soils, as well as accumulation of TEs including Cu, Zn and Cd. Soil samples from active and abandoned oil palm plantations in Sumatra, Indonesia, were analysed for general soil properties as well as TE concentrations. Soils were acidic and low in key nutrients, with production likely to be limited by deficiencies of N, P, K, Mg and Mo, present at some sites in mean concentrations as low as 0.021%, 118 mg kg−1, 778 mg kg−1, 1023 mg kg−1 and 0.095 mg kg−1, respectively. Mean organic C was lower (2.0–3.3%) than reported values in nearby forest soils (7.7%). Soils under palm production contained elevated levels of Cu, Zn, As and Pb up to 38, 91, 9.0 and 28 mg kg−1, respectively, likely due to agrichemical use. The correction of nutrient deficiencies in palm production would require significant fertiliser inputs, which would exacerbate TE accumulation and reduce the net economic revenue from oil production. Our data have shown that in the plantations we have sampled, soils have become degraded. These tropical, weathered, and naturally nutrient-poor soils are ill suited to intensive production that requires high ongoing nutrient inputs. These findings have implications for the sustainability of a regionally significant production system across Southeast Asia.