The rapid increase in global production of and demand for palm oil has resulted in large-scale expansion of oil palm monoculture in the world's tropical regions, particularly in Indonesia. This expansion has led to the conversion of carbon-rich land-use types to oil palm plantations with a range of negative environmental impacts, including loss of carbon from aboveground biomass and soil. Sequestration of soil organic carbon (SOC) in existing oil palm plantations is an important strategy to limit carbon losses. The aim of this study was to investigate SOC stocks of oil palm plantations under different management systems. Soil samples were collected from three different management systems (best management practices (BMP), current management practices typical of large plantations (CMP) and smallholder management practices (SHMP)) in north Sumatra, Indonesia. Plantations were divided into four management zones that were sampled separately with four replicate profiles in the weeded circle, frond stack, harvesting path and interrow zones. All the soil samples were collected from five (0–5, 5–15, 15–30, 30–50 and 50–70 cm) soil depths. Soil samples were analysed for concentration of SOC, soil texture, soil bulk density and pH. Calculations of SOC stocks in the soils were undertaken according to the fixed-depth and equivalent soil mass approaches. Results showed that SOC stocks of plantations under BMP (68 t ha−1) were 31% and 18% higher than under CMP (57 t ha−1) and SHMP (46 t ha−1) respectively. In the BMP system, soils under the interrow zone that received enriched mulch and frond stack positions stored significantly more SOC than the harvesting path of the BMP system (77, 73 and 57 t ha−1 respectively). BMP also had a 33% higher fresh fruit bunch yield compared to the SHMP system. This study shows that residue incorporation or retention as a part of BMP could be an effective strategy for increasing SOC stocks of oil palm plantations and confirms that these management practices could improve yields from SHMP systems.