Increasing soil organic matter content is important in improving soil fertility; however, conventional farming practices generally lead to a reduction in such organic material. A comparative study of organic and conventional arable farming systems was conducted in Shanghai, China, to determine the influence of management practices on soil chemistry, microbial activity, and biomass. Soils used in greenhouses and open field cultivation were obtained from plots subjected to organic farming methods for 3 years or from conventionally farmed fields in the same area. Four combinations of field type and management system were evaluated: (1) organic management in open fields (ORG-OP); (2) conventional management in open fields (CNV-OP); (3) organic management in plastic tunnel fields (ORG-GR); and (4) conventional management in plastic tunnel fields (CNV-GR). Soils obtained at the 0- to 10-cm depth were analyzed using an approach combining traditional soil analysis, microbiological analysis using enzymology and microcalorimetric techniques, and a written survey of management practices among the farmers. Organic management resulted in significant increases (p < 0.001) in total organic C and total N, Olsen-P, cation exchange capacity (CEC), soil respiration, microbial biomass C (C min) and N (N min), and alkaline phosphatase and urease activity. Sucrase activity was highest in CNV-GR soil and lowest in ORG-OP and CNV-OP soils. No significant difference was observed between ORG-OP and CNV-OP. The Olsen-P, total organic C, total N, CEC, N min, and sucrase and alkaline phosphatase activities were greater in greenhouse soils than those under open field cultivation, which indicated a higher level of soil management under greenhouse conditions. The microcalorimetry power–time curves for all samples described typical microbial metabolic activity. In soil samples supplemented with glucose and ammonium sulfate, the heat dissipation per cell unit suggested that microorganisms in soils under organic management had more efficient metabolism. In addition, microbial growth in soils under conventional management displayed lower growth rates, lower peak heat, and longer peak heat times, all of which indicated lower activity of soil microorganisms compared with organic management. There was a large positive correlation (p < 0.01) between the values of P max (the peak value of thermal power), Q total (total heat flux), and k (microbial growth rate constant) and the chemical properties. However, there was a significant negative correlation (p < 0.05) between the value of t max (the time required to reach peak thermal power) and chemical properties other than sucrase activity. Organic production systems significantly improved soil microbial characteristics and increased soil organic C, thus improving soil quality and fertility. Further studies investigating the long-term functional significance of carbon sequestration under organic practices are therefore warranted.