Continuous use of chemical fertilizers and farming practices in rice fields would reduce nutrient availability and biota population in the soil. Because soil biological linkages are sensitive to changes in soil function, changes in fauna and microbial populations can affect soil fertility. This study aimed to identify the condition of soil fertility and soil biota under various farming systems, namely organic, semi-organic, and conventional, and find the indicators that determine soil fertility index (SFI) in the research area. This research is a survey with the sampling method was purposive on the Land Mapping Unit (LMU) overlaid with thematic maps (land use, soil type, slope, and rainfall). The method analysis of SFI using Principal Component Analysis (PCA) and scoring methods were used for the effect of farming systems using One-way, continued by DMRT, and determinant factor using Pearson’s. Correlation. The results illustrated that soil fertility was a moderate category. The highest SFI was in organic rice fields (0.69), then in semi-organic (0.62), and the lowest fertility was in conventional (0.59). Organic farming also showed the best soil biota conditions (0.27 individuals/liter of earthworms and 0.755 µ/g of microbial C biomass) compared to semi-organic (0.15 individuals/liter, 0.508 µ/g microbial C biomass) and conventional farming (0.11 individuals/liter, microbial biomass C 0.325 µ/g). Soil fertility and soil biota are positively correlated, meaning that the higher the soil fertility, the higher the density of soil biota. The soil indicators most determining fertility are total N, P-available, K-available, CEC, and organic C.