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The total area of abandoned and fallow agricultural fields in Japan has been increasing annually. The change in agricultural land use can alter belowground carbon (C) stocks associated with changes in the types of plant species. The aim of this study was to investigate how the cessation of cultivation influenced the soil C storage in former agricultural fields. The study sites were previously used for rice (Poaceae, Oriza sativa L.) and wheat (Poaceae, Triticum L.) cultivation, and fallow management practices had been in effect for three years under three different conditions: two treatments involved mowing and either leaving the plant residue on the ground or removing the plant residue, while the third treatment involved simply abandoning the field. We found that the former paddy site invaded by rhizomatous perennial grasses had significantly higher soil C storage compared to former upland fields that was dominated by annual grass species. The cessation of cultivation increased soil C storage by about 1.3 times in former paddies, and decreased the content by 0.83-0.91 times in former uplands. The three-year total belowground production was 2.0-4.7 times greater in former paddies than former uplands for each management condition, suggesting that lower C input from the annual grasses caused a loss in soil C at the upland fields. Aboveground biomass removal of the perennial grasses strongly reduced C input, whereas the C input from their high belowground production led to the significant increases of soil C storage near the surface of the former paddies. Our studies indicate that high belowground productivity of perennial grasses can increase soil C storage after the cessation of cultivation.