In Japan, rice should be cultivated through sustainable agricultural systems that reduce the use of chemical fertilisers and pesticides. This study investigates the soil fertility of paddy fields under various management practices to evaluate soil fertility in organic farming fields. These results indicate that paddy fields have a higher bacterial biomass and a narrower range of total carbon than orchards and upland fields. Variations in soil fertility can be explained by the similar management practices in paddy fields in Japan. The application of organic fertilisers improved the soil bacterial biomass and total carbon in paddy soils. Moreover, the nutrient contents, including total carbon, total phosphorous, and total potassium, were within suitable ranges for paddy soil fertility. Therefore, instead of using chemical fertilisers, cultivation systems can use organic fertilisers for sustainable development.