A common belief among consumers is the superior quality of organically grown tomato fruits over their conventionally grown counterparts. The present study was performed to evaluate the quality characteristics of tomatoes grown using organic and conventional production systems and to determine the effects of microbial fertilization and plant activators on the tomato fruit quality during storage. Results indicated that firmness, soluble solids, color L and H* values decreased significantly in all treatments during storage. However, total soluble and reducing sugars and color C* value significantly increased in both organically and conventionally grown fruit during storage. Application of plant activator and microbial fertilizer and their combination significantly affected the trend of changes in quality parameters but these effects were cultivar dependent rather than growing system. The data suggest that organically produced fruit maintain their quality during storage for a period comparable to that of conventionally grown fruit. Although certain quality parameters remain higher either in organically or in conventionally grown fruit during storage, these effects seem to be cultivar dependent.