The soil fertility of agricultural fields is highly influenced by land use systems such as cultivated crops. In this study, the soil fertilities of upland and paddy fields were compared using the soil fertility index (SOFIX). The SOFIX database of 795 agricultural fields showed that the average bacterial biomass was higher in paddy fields than in upland soils despite the low level of organic matter in paddy field soils. The difference in soil properties between upland and paddy fields might be influenced by water management, cropping system, and fertilizers. Based on the bacterial biomass and total carbon (TC), the agricultural fields were divided into four groups and each group corresponded to a particular type of agricultural management. One group with high bacterial biomass and high TC seemed to be related to the appropriate use of organic fertilizers without agrochemicals. The values of SOFIX parameters of this group were suitable to maintain the optimum level of microbial abundance and activities. The optimal conditions for the upland and paddy field soils were determined based on the SOFIX database.