Depending on the type of agricultural use and applied crop rotation, soil organic carbon accumulation may depend, which can lead to less CO2 fixation in the global carbon cycle. Less is known about organic carbon emissions in different crop production systems (cereals, grasses) using different agrotechnologies. There is a lack of more detailed studies on the influence of carbon content in the soil on plant productivity, as well as the links between the physical properties of the soil and the absorption, viability, and emission of greenhouse gases (GHG) from mineral fertilizers. The aim of this study is to estimate the long-term effect of soil organic carbon sequestration potential in different crop rotations. The greatest potential for organic carbon sequestration is Norfolk-type crop rotation, where crops that reduce soil fertility are replaced by crops that increase soil fertility every year. Soil carbon sequestration potential was significantly higher (46.72%) compared with continuous black fallow and significantly higher from 27.70 to 14.19% compared with field with row crops and cereal crop rotations, respectively, intensive crop rotation saturated with intermediate crops. In terms of carbon sequestration, it is most effective to keep perennial grasses for one year while the soil is still full of undecomposed cereal straw from the previous crop. Black fallow without manure fertilization, compared to crop rotation, reduces the amount of organic carbon in the soil up to two times, the carbon management index by 2–5 times, and poses the greatest risk to the potential of carbon sequestration in agriculture.