In tropical deltas, intensive monoculture with three rice crops per year (RRR) has been the standard for decades. However, in recent years some farmers have started rice-based rotations with one or more upland crops per year. The trends for increased grain yields with this new system raises the question as to whether the introduction of upland crops affects properties of alluvial clay paddy soil. This was evaluated in the present study, which was performed at 40 paddy fields in the Vietnamese Mekong Delta under four different cropping systems (10 farms per system) on paddy rice soils: RRR; crop rotation with two rice crops and one upland crop per year (RUR); crop rotation with one rice and two upland crops per year (RUU); and upland crop (UUU). Soil samples were collected at depths of 0–10, 10–20 and 20–30 cm. Most soil properties differed significantly between the RRR and the RUR, RUU or UUU. The RUR, RUU and UUU systems alleviated soil compaction, resulting in reduced penetration resistance and bulk density and increased total and macroporosity at 20–30 cm depth. In addition, aggregate stability index and plant-available water capacity were higher for RUR, RUU and UUU compared with RRR at the 20–30 cm depth. Average soil organic carbon (SOC) stocks ranged from 59.3 t ha–1 in UUU to 72.3 t ha–1 in RUR, with SOC stocks in RRR and RUU being intermediate (66.4 and 68.3 t ha–1) and not significantly different to that of the RUR system. Carbon hydrolysable by HCl (Chydrolysable) was 74–84% greater in the RUR, RUU and UUU than in RRR systems. In conclusion, rice–upland crop systems may alleviate soil degradation resulting from continuous rice monoculture.