Forest degradation and conversion of forested land to agriculture may lead to changes in soil properties and soil fertility losses. An undisturbed and a degraded forest, and eight different agricultural rotation systems were selected in the Chitawan district to document differences in soil quality due to land-use changes. The results showed that soil fertility as expressed by organic carbon, total nitrogen, and cation exchange capacity decreased when natural productive forest was converted into agriculture. There was also a decline in soil quality when natural forests became degraded and over-utilized. Exchangeable bases, aluminum, pH, and compaction were significantly affected. Some of the very intensively cultivated soils under innovative triple-crop rotations showed that soil quality can be improved to conditions that are superior to those found under degraded forests.