This study investigated the influence of species, capture method, chilling, and freezing on the quality and variations in biogenic amines of Thunnus tonggol and Thunnus albacares. Samples were collected from different sources, including fisheries ports, cold rooms, and canning factories. The results indicated that canned fish had significantly higher levels of biogenic amines, especially histamine, compared to raw fish from ports and cold rooms. However, all canned samples complied with the FDA regulation of 50 mg/kg for histamine content. Canning led to a substantial increase in total amines, with histamine being the predominant amine in most groups. Putrescine was present in all samples, with the highest levels found in canned tuna made from frozen yellow-fin tuna captured using drift gillnetting. Canned samples also exhibited higher cadaverine levels compared to raw tuna. Storage conditions, capture method, and tuna species were found to significantly affect tuna quality and biogenic amines formation.