Compared to natural vegetation, cropland soils are depleted in soil organic carbon (SOC). When soil is converted from natural land or semi-natural land, such as forests, woodlands, grasslands, steppes, and savannas, the SOC content in the soil reduces by about 30–40%. This loss is due to the removal of plant material containing carbon, in terms of harvests. When land use changes, the carbon in the soil will either increase or decrease, and this change will continue until the soil reaches a new equilibrium. Deviations from this equilibrium can also be affected by variated climate. 
The decreasing of SOC content can be counteracted by increasing the carbon input. This can be done with several strategies, e.g. leave harvest residues on the field, use manure as fertilizer, or including perennial crops in the rotation. Perennial crops have a larger below ground biomass fraction, which increases the SOC content. 
Perennial crops reduce the need for tillage and thus help mitigate soil erosion, and may help increase soil organic matter. Globally, soils are estimated to contain >8,580 gigatons of organic carbon, about ten times the amount in the atmosphere and much more than in vegetation. 
Researchers have found that rising temperatures can lead to population booms in soil microbes, converting stored carbon into carbon dioxide. In laboratory experiments heating soil, fungi-rich soils released less carbon dioxide than other soils.
Following carbon dioxide (CO) absorption from the atmosphere, plants deposit organic matter into the soil. This organic matter, derived from decaying plant material and root systems, is rich in carbon compounds. Microorganisms in the soil break down this organic matter, and in the process, some of the carbon becomes further stabilized in the soil as humus - a process known as humification. 
On a global basis, it is estimated that soil contains about 2,500 gigatons of carbon. This is greater than 3-fold the carbon found in the atmosphere and 4-fold of that found in living plants and animals. About 70% of the global soil organic carbon in non-permafrost areas is found in the deeper soil within the upper 1 meter and stabilized by mineral-organic associations.