This study investigated the effects of reduced and conservation tillage, namely two-layer ploughing (LP) and layer-cultivating (LC) on soil ecological properties (physical, chemical, microbiological) in an organic farming system relative to ploughing (P). As a major trend, the amounts of soil organic C, microbial biomass C and N, the Cmic to Corg ratio, and microbial activity increased at 0-15 cm depth in the order P - LP - LC while they decreased at 15-25 cm depth in the same order, both in green fallow and winter rye plots. For example, at 0-15 cm depth, soil microbial biomass C concentration was significantly 25% (LP) and 30% (LC) greater in green fallow plots and 18 to 20% greater in winter rye plots than in P. This was highly correlated with an increase in aggregate stability at these sites. Non-ploughing also resulted in a significantly higher bulk density. In addition, the amounts of ergosterol were higher at 0-15 cm depth in LP and LC treatments than in P. Hence, it is indicated that the microbial community changed towards fungi at 0-15 cm depth in reduced and conservation tillage plots. It can be concluded that reduced or conservation tillage in organic farming systems has beneficial effects on soil organic matter, microbial biomass, and activity.