Colatura di alici di Cetara is a fish sauce obtained from the fermented seasoning of anchovies (Engraulis encrasicolus L.) in salt and produced in the province of Salerno (Campania, Italy). The anchovies used in its production could indicate the degree of the ecosystem's well-being through the study of heavy metals. Histamine represents one of the major hygienic and health concerns in fish products belonging to the Engraulidae family and those derived from them through enzymatic maturation. The current study aimed to: i) investigate the levels of heavy metals in anchovies; and ii) assess histamine content in two distinct production processes: the first following the Protected Designation of Origin (PDO) protocol, which involves anchovy’s evisceration; and the second employing an experimental protocol using whole anchovies. The determined parameters were: i) heavy metals cadmium (Cd) and lead (Pb) using an atomic absorption spectrophotometer and mercury (Hg) using a direct mercury analyzer on the raw material (T0), coarse salt, and processed anchovies at T1; ii) polycyclic aromatic hydrocarbons (PAHs) using a high-performance liquid chromatography (HPLC) coupled to fluorescence detection at T1; and iii) histamine using an ultra HPLC-diode-array detection analysis at all stages throughout the process (T0 to T8). The results of the heavy metals analyzed show values below the permitted limits for Cd (0.013±0.006 mg/kg), Pb (not detected), and Hg (0.072±0.003 and 0.043±0.026 mg/kg). The PAHs were not detected. All histamine concentrations determined were below the maximum limit set by the European legislation for fish sauces. The highest values were found in the anchovies gutted at T2 (0.86±0.08), in the respective colatura (51.00±1.70) of the PDO procedure, and in the experimental procedure at T8 (7.00±0.60). No significant differences were found between the colatura obtained by both production processes. The study highlighted the importance of raw material selection and monitoring of the process for producing a product like Colatura di Alici di Cetara.