Forest and grassland soils in north-eastern Iran are being degraded and destroyed by inappropriate agricultural activities. This study investigated effects of land-use changes on several indicators of soil quality (SQ) in this area. We found higher organic carbon (OC) and total nitrogen (N) contents in virgin soils (under forests and pastures) than in cultivated soils. Distribution of OC throughout the soil profile was influenced by the type and length of tillage operations performed at different sites. Cultivation reduced OC content of the subsoil (0.50–1.00 m) and contributed to a more uniform distribution of organic matter in the plough layer (0–0.50 m) by mixing upper and lower horizon soils and incorporating of organic inputs to a greater depth. In 4 of 5 sites, tilled soils had lower ECe and SAR values than the virgin soils, but when the water table was near the soil surface, the ECe and SAR values were higher in cultivated sites. This suggests that when the water table is deep, the quality of salt-affected virgin soils may be improved by cultivation and leaching of excess salts to deeper layers. In 4 of 5 sites, the virgin soils had slightly greater clay content than the tilled soils, but these soils also had 41–89% less dispersible clay than their cultivated counterparts. The virgin soils had 2–31-fold greater aggregate stability, 4–33% lower bulk density, 6–31% higher water-holding capacity (at 0.3 bar suction), higher cation exchange capacity (CEC), and higher respiration rate than the cultivated soils. The results of this study indicate that frequent tillage and use of summer fallow deteriorates SQ by decreasing SOC and enhancing soil erosion through decreased structural stability and increased mechanically dispersible clay. The results stress the need for farming practices that preserve OC in soils in order to reduce flooding and erosion risks.