Soil organic carbon storage (SOCS) is one of indicator for soil quality. It requires several years to be able to detect the SOCS and the impact on crop yields. A research was conducted to study soil organic carbon (SOC), labile carbon (SLC), SOCS and the yields of Chinese cabbage (Brassica chinensis L.) under organic and conventional farming systems. The location was at the area of vegetable farming in Baturiti village, Tabanan regency, Bali province, Indonesia, between 08032’93”SL and 115017’64”EL, 975 m above sea level. Soil samples were taken from the land of organic system after one, three and five years of application, and from the conventional system accordingly in the neighboring area. Variables of SOC, SLC, SOCS, total nitrogen, soil respiration and bulk density were measured. The yields of Chinese cabbage were obtained from the last five years of farmer records. Results of this study indicated that SOC, SLC, SOCS, total nitrogen and soil respiration, but not soil bulk density, were significantly (P<0.05) higher under organic than under its conventional counterpart after five years application of organic system. The SOCS increased 3.37 Mg C ha-1 annualy under organic compared to that under conventional system. The SOC, SLC and soil microbial respiration significantly 68.6%, 49.01% and 38.5% higher respectively under organic farming system after five years, but soil nitrogen did not increase. The organic system was highly correlated (r= 0.836**, r=0.846**) with levels of SOC and SLC respectively. During the first three years the yield of Chinese cabbage was lower under organic but after five years the yields (25.78 t ha-1) was not significantly different from that in conventional system. This explains that significant yield increases in organic farming system could only be expected after five years of application. Keywords: Soil organic carbon, soil organic carbon storage, labile carbon, organic farming system, conventional farming system, Chinese cabbage (Brassica chinensis L.)