The objectives of this study were to evaluate the effect of nitrogen nanobubble for storing fresh yellowfin tuna (Thunnus albacares). Yellowfin tuna were stored for 10 days in two types of treatment: nitrogen nanobubble (NNB) and conventional packaging process (CPC). Two methods including qualitative (organoleptic) and quantitative (histamine and mercury content, and total plate count of bacteria) were analyzed to determine the treatments effect on post-harvest quality, microbial population, and shelf-life of the fish. Results show that nitrogen nanobubble is proven to maintain dissolved oxygen levels remain in low conditions ( < 1 mg/L) during treatment. Although the organoleptic properties for both treatments do not show any significant differences, the lowest histamine and mercury contents are found in treatment NNB at 11.8 mg/kg and 0.14 mg/kg, respectively. The microbes in treatment NNB is achieved levels deemed safe (based on national standards) at 1.8 × 104 colonies/g, E. coli content <3 MPN/g, and the presence of Salmonella sp. are not detected. Our results suggest that treatment NNB is preferable for preservation process of fresh yellowfin tuna and might improve to extend the shelf-life.