Considerable amounts of soil organic matter (SOM) are stabilized in paddy soils, and thus a large proportion of the terrestrial carbon is conserved in wetland rice soils. Nonetheless, the mechanisms for stabilization of organic carbon (OC) in paddy soils are largely unknown. Based on a chronosequence derived from marine sediments, the objectives of this study are to investigate the accumulation of OC and the concurrent loss of inorganic carbon (IC) and to identify the role of the soil fractions for the stabilization of OC with increasing duration of paddy soil management. A chronosequence of six age groups of paddy soil formation was chosen in the Zhejiang Province (PR China), ranging from 50 to 2000 years (yrs) of paddy management. Soil samples obtained from horizontal sampling of three soil profiles within each age group were analyzed for bulk density (BD), OC as well as IC concentrations, OC stocks of bulk soil and the OC contributions to the bulk soil of the particle size fractions. Paddy soils are characterized by relatively low bulk densities in the puddled topsoil horizons (1.0 and 1.2 g cm− 3) and high values in the plow pan (1.6 g cm− 3). Our results demonstrate a substantial loss of carbonates during soil formation, as the upper 20 cm were free of carbonates in 100-year-old paddy soils, but carbonate removal from the entire soil profile required almost 700 yrs of rice cultivation. We observed an increase of topsoil OC stocks from 2.5 to 4.4 kg m− 2 during 50 to 2000 yrs of paddy management. The OC accumulation in the bulk soil was dominated by the silt- and clay-sized fractions. The silt fraction showed a high accretion of OC and seems to be an important long-term OC sink during soil evolution. Fine clay in the puddled topsoil horizon was already saturated and the highest storage capacity for OC was calculated for coarse clay. With longer paddy management, the fractions < 20 μm showed an increasing actual OC saturation level, but did not reach the calculated potential storage capacity.