The economic benefits of organic agriculture and its wide adoption are well documented, but the impact of that practice on soil C dynamics in irrigated croplands of semi-arid regions is less well understood. In manure-based organic production systems, land applications of animal wastes not only provide nutrients but could also contribute to soil carbon sequestration. A study was conducted in irrigated cotton (Gossypium arboreum L) agro-ecosystems of New Mexico (USA) under conventional (CONV; 100kgN/ha as urea and NH4NO3) and organic farming practices (OF for 3-9yr; 50Mg dry manure/ha) to assess the effect of OF on soil C stocks (organic, inorganic) and biochemical indices [microbial biomass C (MBC); respiration; metabolic quotient (qCO2)]. In the plough layer (0-30cm), soil organic carbon (SOC) stocks tended to be higher (although not statistically) under OF (35.9Mg C/ha) than CONV (33.5Mg C/ha). However, when the entire 100-cm soil profile was considered, the total SOC under CONV exceeded that under OF by 39.8Mg C/ha, but this may be influenced by other factors. Accounting for 52% of the total C stock, inorganic C was significantly higher under CONV than OF and was positively correlated with soil respiration and the H/C ratio of soil organic matter. While OF duration had no consistent effect on soil biochemical properties, MBC was significantly higher (1.5 times) and the qCO2 (3-6 times) was lower in the organically fertilized soils than under CONV. These results suggest the development, under OF, of a soil microbial community that is larger and processes added C substrates more efficiently compared with the community present in CONV practices.