In the Mekong Delta, alluvial clay soils have been used intensively over many generations for rice monoculture. Currently, farmers are confronted by problems of declining land productivity. Rotations comprising rice and upland crops can increase soil quality, but appropriate cropping systems for paddy soils have received relatively little attention. We therefore established a multiyear field experiment to evaluate the long-term effects of cropping systems with different rotations on soil chemical quality. Systems laid out in a randomized complete block design with four replications were as follows: (i) traditional rice monoculture with three rice crops per year (R-R-R), (ii) rotation with two rice crops and maize (R-M-R), (iii) rotation with two rice crops and mung bean (R-Mb-R) and (iv) rotation with one rice crop and two upland crops – mung bean and maize (R-Mb-M). We hypothesized that systems with rotations of upland crops and their temporary beds improve chemical quality of paddy rice soil. Soil chemical parameters were determined to better understand and evaluate the sustainability of the cropping systems. Results showed an improvement in soil chemical quality for cropping systems with rotations of rice and mung bean or maize grown on temporary beds (R-M-R, R-Mb-R and R-Mb-M), particularly the content of soil organic carbon and a presumed hydrolysable labile carbon fraction compared with rice monoculture. Less pronounced improvements in EC, CEC and total acidity were also found with inclusion of upland crops. Cropping systems of rice with upland crops improved rice grain and straw yield in subsequent season in contrast with rice monoculture.