The soil fertility of rice fields is closely related to rice crop production. The research aims to identify soil fertility under different rice field farming systems, find the key factor of soil fertility, and recommend strategies to improve soil fertility based on the key factor. The research was conducted in Nguntoronadi District, Indonesia, on conventional, semi-organic, and organic rice fields. The research was an exploratory descriptive survey through a field survey approach and soil chemistry and physics analysis. Soil sampling was conducted in 12 Land Map Units (LMUs) with three replicates using purposive sampling methods. Observation indicators include soil pH, organic C, total N, C/N ratio, available P, available K, exchangeable Ca, exchangeable Mg, Cation Exchangeable Capacity (CEC), Base Saturation (BS), Aluminum saturation, soil texture, and worm population density representing soil chemical, physical, and biological properties. Soil fertility is determined using Principal Component Analysis (PCA) and scoring based on the category. The research results show that the level of soil fertility under various rice field farming systems was included in the moderate with ranges of 0.53-0.70, and organic farming has the highest soil fertility. The key factors of soil fertility include pH, organic C, available P, available K, Ca-dd, CEC, and Aluminum saturation. The appropriate management direction is the addition of organic fertilizer in the planting period.