SummaryThe objective of this research is to investigate the impact of different hydrolysis (chemical, enzymatic and microbiological) methods of Bigeye tuna waste (Thunnus obesus) on yield, degree of hydrolysis (DH), chemical composition, amino acid profile, functional properties and microbial quality of FPH produced. The enzymatic technique produced the highest yield (11.04%) and the greatest DH (39.04%) while it gave the lowest average peptide chain length (2.56) (P < 0.05). Also, protein and fat (76.37% and 10.82%, respectively) were the highest in the enzymatic hydrolyzed fish (FPH‐E) followed by microbial fermentation (FPH‐M) (P < 0.05). In FPH‐E, FPH‐M and chemical fish protein hydrolysates (FPH‐C), the essential to non‐essential amino acid ratios were 2.43, 1.79 and 0.51, respectively. They also had good functional properties, although they were less than FPH‐C in terms of water binding capacity (3.47 and 4.18 g g−1), oil binding capacity (9.84 and 7.38 g g−1) and foaming capacity (25% and 30%, respectively), and their foam stability rate was high. All FPHs products had a low range of microbial counts, with the FPH‐M exhibiting the greatest total count of bacteria, lactic acid bacteria and moulds and yeasts. Therefore, the biologically extracted FPH especially FPH‐E has the best compositions and qualities, making them an alternative ingredient for fish meal in fish feed formulation.