Organic farming systems based on ecological concepts have the potential to produce sustainable crop yields with no decline in soil and environmental qualities. Recent expansion of sustainable agricultural systems, including organic farming, has brought about need for development of sustainable farming systems based on value judgments for key properties of importance for farming. Chemical and microbiological properties were chosen as indicators of soil quality and measured at soil depth intervals of 5-20 and 20-35 cm in conventional and organic-based apple orchards located in Yeongchun, Gyeongbuk. The orchards were two adjacent fields to ensure the same pedological conditions except management system. Soil pH in organic farming was around 7.5, whereas below 6.0 in conventional farming. Organic farming resulted in significant increases in organic matter and Kjeldahl-N contents compared to those found with conventional management. Microbial populations, biomass C, and enzyme activities (except acid phosphatase) in apple orchard soil of organic farming were higher than those found in conventional farming. Higher microbial quotient ($C_{mic}/C_{org}$ ratio) and lower microbial metabolic quotient for $CO_2(qCO_2)$ in organic farming confirmed that organic farming better conserves soil organic carbon. Biological soil quality indicators showed significant positive correlations with soil organic matter content. These results indicate organic-based farming positively affected soil organic matter content, thus improving soil chemical and biological qualities.