Cultivation of irrigated desert soils in Central Iran is one way of utilizing under-exploited land to produce more food. This study explores the value of soil quality indicators as measures when converting desert to croplands. Soil samples from unfarmed desert, wheat and alfalfa sites in the Abarkooh Plain (Central Iran) were taken from 0–10, 10–20 and 20–30 cm depths. Soil quality indicators including organic carbon, total nitrogen, carbohydrate, particulate organic carbon (POC) in aggregate fractions, and aggregate water-stability were determined. The desert soils contained organic carbon of 0·26–0·56 g kg−1, total nitrogen of 0·05–0·08 g kg−1 and carbohydrate of 0·03–0·11 g kg−1 at 0–30 cm depth. Across this depth, the contents of organic carbon, total nitrogen and carbohydrate in wheat were about 3–7, 2–3 and 6–26-times higher than those of desert soils, respectively. These values for alfalfa were 5–12, 3–4 and 7–35 times, respectively. The POC (near zero in desert soils) and generally other soil quality indicators showed greater improvement in alfalfa than in wheat fields. The results indicated a significant decrease in proportion of the fraction <0·05 mm in cultivated soils, whereas the proportion of the large aggregate size classes (2–4 and 1–2 mm) was increased by irrigation and cultivation. A significant improvement in aggregate water-stability was observed in cultivated soils. At all depths, a large portion of the total soil organic carbon was stored in the fractions <0·05 mm for desert and macroaggregates (0·25–2 mm) for cultivated soils. Copyright © 2010 John Wiley & Sons, Ltd.