The economic viability of cocoa and its shade-loving character made it a successful intercrop in oil palm (OP) plantations. However, its effect on soil properties, especially physical properties, is not fully understood in OP based cropping system. Two cropping systems (OP monoculture and OP + cocoa intercropping) at two sampling points (basins and interspace) and five soil depths (0–20, 20–40, 40–60, 60–80 and 80–100 cm) were considered in the study. This investigation sought to quantify the effects of intercropping in OP plantations on bulk density, aggregate stability, total organic carbon (TOC), total nitrogen (TN), glomalin-related soil protein (GRSP), aggregate-associated TOC, TN and carbon preservation capacity (CPC) of the aggregate fractions. Compared to OP monoculture, cocoa intercropping in OP plantations significantly improved the geometric mean diameter (GMD) of the aggregates by 12.70%–64.00%, aggregate stability index (ASI) by 9.87%–24.00%, TOC by 6.80%–49.70%, TN by 3.00%–28.10% and GRSP by 11.80%–54.60%. Under intercropping, the TOC and TN contained in different aggregate fractions also improved. Small macroaggregate fractions were the aggregate fractions with the greatest capacity to store carbon (3.27–16.60 g kg^–1). Furthermore, intercropping increased the CPC of the soil aggregates, particularly micro and macroaggregates, by 1.88%–71.00%. The study suggested that intercropping cocoa in OP plantations is a sustainable strategy to enhance soil health and maximise carbon sequestration.