According to Article 3.4 of the Kyoto Protocol, agricultural soil could be used as a sink for carbon sequestration. Soil sequestration of carbon provides dual benefits: an increase in soil productivity and a reduction in atmospheric carbon concentration. The gain in soil productivity is a slow process and attaining a steady-state level of carbon in soil takes several years. A frequently encountered difficulty in this situation is how to discount the future benefit of carbon sequestration into a current term. We compared the net benefit of four alternative management systems using discount rates based on the sliding gamma distribution, market rate of investment, and the social rate of time preference. We also calculated the sustainability of these alternate management systems based on the profitability and productivity index and their capacity to maintain the natural capital in soil. The result indicated that a management system that combines no-till and an organic source of nutrients is the most attractive system based on carbon sequestration, total discounted net present value, and sustainability perspectives.