The objective of present research is to evaluate the changes in the chemical, microbial, and biogenic amines in Persian fish sauce (Mahyaveh) during 40 days of fermentation. In the current survey, the parameters of salt percentage, pH, total nitrogen concentration, amino nitrogen concentration, Brix, color features, cadaverine, and histamine concentration were measured in the fish sauce. The amino nitrogen content, total protein, Brix, and salt were increased along with the progression of fermentation process. The microbial population of Mahyaveh sauce demonstrated that lactic acid bacteria (LAB), total bacterial count, and Enterobacteriaceae decreased during fermentation. The population of lactic acid bacteria and the total count of bacteria were around one logarithmic cycle lower in the presence of 10% salt than under low salt conditions. Histamine and cadaverine concentrations increased to 43.49 and 42.76 mg/kg during the fermentation period, respectively. As a result, the population density of histamine‐producing bacteria rose from 3.00 log CFU/mL at the beginning to 4.58 log CFU/mL at the end of process. The population density of cadaverine‐producing bacteria was 3.43 and 5.24 log CFU/mL on the 20th and 40th days of fermentation, respectively. Sensory evaluation results indicated that our sample of fish sauce had an overall acceptability score of 5.1 (good). On the other hand, Principal Component Analysis (PCA) demonstrated a positive correlation between the most of chemical parameters and the fermentation period. The concentration of cadaverine and histamine has a positive association with the pH and type of bacteria producing the biogenic amines.