<p>Soil carbon sequestration is a long-time storage of carbon in soil which represents 70% of the carbon in land. Therefore, the main aim of this study is to investigate the effect of the agricultural practice systems on the soil carbon sequestration and properties, productivity, water consumption, soil carbon sequestration, CO₂ emission and cost of some agricultural crops. To achieve that, different farming systems (conventional, organic and biodynamic) and four crops (maize, tomato, faba bean and potato) were used during 5 agricultural years. The obtained results indicated that, the agricultural practices for different farming systems enhanced the soil properties. Biodynamic practice farming causes reduction in bulk density, which it increase the water holding capacity of the soil which in turn decreased the water consumption by plants. Regarding the chemical properties of the soil, biodynamic and organic farming improved the chemical characteristics such as pH, EC, N, P and K compared to the conventional practice farming. Yield values of both biodynamic and organic farming system were higher than that of the traditional farming system. The amount of soil carbon sequestration ranged from 1980.17 to 4782.82, 2505.89 to 6132.38 and 1581.07 to 5986.25&#xa0;kg ha^− 1 for conventional, organic and biodynamic systems, respectively. The amount of CO₂ emission reduction for organic and biodynamic systems was higher than those of conventional system during experimental period. The highest value of carbon profit (13,071.60 Egyptian pound per hectare (EGP ha^− 1), $=48.48EGP) was found with the biodynamic system. The highest values of total net profit were 25,046.64, 67,463.04, 44175.84 and 94,674.24 EGP ha^− 1 for maize, tomato, faba bean and potato crops, respectively, were found with the organic farming system after 5 agricultural years.</p>