SummaryMost organic farmers in South Korea use a synthetic plastic film mulch to control weeds, plus high amounts of organic nutrients sourced from outside the cropping area, due to a lack of information on crop rotations using legume or deep-rooting cover crops. We have evaluated the effects of cover crop rotation on soil and plant nutrition during red pepper (Capsicum annuum L.) production from 2002 to 2005. The four treatments applied were: (i) a conventional farming (CF) system without cover crop rotation, or (ii) three organic farming (OF) systems, which either rotated the annual production of red peppers with hairy vetch (OF+HV), or rye (OF+R) from 2002 to 2004, or had an alternating cultivation of rye in 2002 and in 2004 with hairy vetch in 2003 (OF+R-HV). The OF+R system increased the below-ground biomass [39 MT ha–1, fresh weight (FW)] of the rye cover crop, but the above-ground biomass of the cover crop (22 MT ha–1 FW) was similar to those in the OF+HV and OF+R-HV systems. All OF systems, especially OF+HV, increased the soil pH, as well as P, K, Ca, and Mg concentrations to a soil depth of 0 – 20 cm in 2003, and pH, total-N, and K concentrations in 2005. Soil pH, electrical conductivity, and macro-nutrient concentrations decreased from 20 – 100 cm soil depth. All three OF systems reduced the bulk density of the soil and increased soil porosity compared to the CF system. Higher mineral nutrient concentrations in plants grown in the CF system compared to the three OF systems occurred only for Mg in 2003. The CF system increased marketable fruit yields, but did not increase the annual gross income. The highest crop value was observed in the OF+HV system. There was a net loss of N (–9 kg ha–1) in the OF+HV system in all 3 years, while the OF+R system had the highest positive balance level of N (54 kg ha–1).Therefore, the leguminous cover crop (hairy vetch) was useful as a green manure to increase annual gross incomes, increase N-use efficiency, and reduce soil N losses.