Soil carbon sequestration is a riskier long-term strategy for climate mitigation than direct emissions reduction, but it plays a main role in closing carbon emission gaps. Effects of long-term cultivation on soil carbon sequestration were studied at the western edge of the Nile Delta near Alexandria, Egypt. Seven agricultural fields of different ages (0–50 years in use) were selected and compared with the surrounding desert (virgin soil) and desert shrub-land. Samples were taken at three horizons, 0–30, 30–60, and 60–90 cm, and tested for differences in physical and chemical properties. The results of long-term cultivation reveal that the European Commission (EC) value was 11.77 dS/m in virgin soil, while the EC values decreased to 5.82, 4.23, 3.74, 2.40, and 2.26 dS/m after 5, 10, 20, 30, and 50 years of cultivation, respectively. The calcareous rock fraction smaller than 50 μm in size revealed another phenomenon, where active calcium carbonate content increased with cultivation practices from 1.15% (virgin soil) to 5.42%, 6.47%, 8.38%, and 10.13% after 5, 10, 20, and 30 years of cultivation, respectively, while shrub-land also showed a low amount of active CaCO3 with 1.38%. In fifty years of cultivation, soil bulk density decreased significantly from 1.67 to 1.11 g/cm3, and it decreased to 1.65, 1.44, 1.40, and 1.25 g/cm3 after 5, 10, 20, and 30 years, respectively. These results reveal that the increase in soil carbon stock in the upper 90 cm amounted to 41.02 tons C/ha after five years of cultivation, compared to virgin soil with 13.47 tons C/ha. Soil carbon levels increased steeply during the five years of cultivation, with an average rate of 8.20 tons C/ha per year in the upper 90 cm. After the first five years of cultivation, the carbon sequestration rate slowed, reaching 4.68, 3.77, 2.58, and 1.93 tons C/ha per year after 10, 20, 30, and 50 years, respectively, resulting in sequestration-potential values of 46.78, 75.63, 77.43, and 96.45 tons C/ha. These results indicate that potential soil carbon sequestration resembles a logarithmic curve until the equilibrium state between carbon application and decomposition by microorganisms is reached.