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A large proportion of soil located in semi-arid and arid regions contain high levels of carbonates or soil inorganic C (SIC). This SIC pool may be affected by agricultural activities and thereby influence the global C balance. The purpose of this study was to examine the total (pedogenic) soil C stock in agroecosystems under cultivation for 300 years in the southern forest-steppe ecotone in central Russia. Grey forest soils (Luvisols) under broad-leaved deciduous forest dominated this area prior to cultivation. Our results showed that the pedogenic C stock increased 15-50% due to an accumulation of SIC in the top 200 cm as a result of agricultural activities. A ~10% increase in SOC was also observed in agricultural soils cultivated for more than 200 years. A quantifiable increase in carbonate content in association with the 14C-age of the newly-formed carbonates suggested that changes in the hydrothermal regime of arable lands led to an upward movement of carbonates from the parent material. This upward movement may have occurred via capillary-sized pores in colloidal suspensions. This led to the movement of carbonates without the exchange of young soil CO2. Our results suggested that the upward movement of carbonates may be a rapid soil transforming process taking place over less than 50 years. The pedogenic C stocks (0-200 cm) in this region’s agricultural and forest lands were estimated to be ~11.5 Gt C, of which one third was SIC. We postulated that SIC in agricultural soils was safely deposited and highly protected from dissolution because carbonates were located in the smallest pores and impregnated the soil mass according to micromorphological observations.