Filleting effect of refrigerated bonito with and without ice on the quality changes and food safety was investigated. Significant variations occurred (P < 0.05) in sensory, chemical and microbiological values amongst groups. The best sensory results were found for filleted bonito with ice (FBRI) with a shelf-life of 13 days. While sensory values decreased significantly during storage, opposite situation occurred for both chemical and microbiological results (P < 0.05). The lowest total volatile basic nitrogen value was also observed with FBRI and was within the acceptable levels for 15 days as 17.86 mg 100 g−1. All samples contained acceptable trimethylamine levels for 15 days despite unacceptable sensory values after certain days. Although filleting seemed to increase the lipid oxidation, ice application resulted in lowering thiobarbituric acid content. Histamine results closely supported sensory values in terms of legally permitted levels usually by set FDA. While WBR contained histamine value over EU permitted level as 113.78 ppm on the 7th day, the value for FBRI was 56.13 ppm on the 15th day. Histamine-forming bacteria counts supported histamine formation in most groups, while total bacteria counts were in agreement with sensory results. This study suggests that using ice and filleting can improve shelf-life of bonito stored at refrigerated temperatures in terms of food quality and safety.