Labile fractions of soil organic C (SOC) can respond rapidly to changes in C supply and are considered to be important indicators of soil quality. An attempt is made in this paper to investigate into the dynamics of total organic C (C tot), oxidisable organic C (C oc), very labile C (C frac 1), labile C (C frac 2), less labile C (C frac 3), non-labile C (C frac 4), microbial biomass C (C mic), mineralizable C (C min) and particulate organic C (C p) in relation to the system productivity of a 20-year-old rice (Oryza sativa L)–berseem (Trifolium alexandrium L) cropping system with different management strategies [no fertilization, only NPK and NPK + FYM (farmyard manure) applied in different seasons] in the hot humid, subtropics of India. Cultivation over the years caused a net decrease, while balanced fertilization with NPK maintained the SOC. About 62% of the C applied as FYM was stabilized into SOC. The passive pool (C frac 3 + C frac 4) constituted about 55% of the C tot. A larger proportion (63%) of applied C was stabilized in the passive pool of SOC. Of the analysed pools, C frac 1, C mic, C p and C min were influenced most by the treatments imposed and explained higher per cent variability in the yield of the crops.