This study was conducted to determine the suitable soil conditions for tomato cultivation under an organic farming system. Tomatoes were cultivated in chemically and organically fertilized experimental fields from 2013 to 2015 in Moriyama City, Shiga prefecture, Japan. Organically and chemically fertilized soils had different total carbon (TC) and total nitrogen (TN) contents, and different carbon-to-nitrogen ratios (C/N ratios). The tomato yields varied from 1290 to 5960 kg/0.1ha in the organically fertilized fields. The organic soil conditions for the highest tomato yield showed a TC content of ~33,000 mg/kg, TN content of ~1600 mg/kg, and a C/N ratio of ~21. The yield was reproducible in the organic fields under similar values of TC, TN, and C/N ratio in the soil. Significantly higher nitrogen and phosphorus circulation activities were observed in the high-yielding fields. Appropriate control of TC, TN, and C/N ratio is necessary for the enhancement of both microbial activity and tomato yield. Values of the important tomato quality parameters (lycopene, glutamic acid, and acid content) were also increased in the high- yielding tomato fields. We therefore suggest that a suitable soil condition for improving both the yield and quality of tomatoes in an organic farming system is TC of 30,000 - 36,000 mg/kg, TN of 1600 - 1900 mg/kg, and a C/N ratio of 18 - 21.