The aim of this study was to investigate the survival of Salmonella Enteritidis, Staphylococcus aureus and Listeria monocytogenes in salted and marinated anchovy (Engraulis encrasicholus). Total viable counts (TVCs), lactic acid bacteria, Enterobacteriaceae, and yeasts/molds were also enumerated. Initially, TVC was as high as 5.5 log10 cfu/g, but the population dropped down to 3.2 and 2.2 log10 CFU/g for salted and marinated anchovy, respectively. S. aureus was the most salt‐tolerant and L. monocytogenes was the most acid‐tolerant microorganism. A biphasic inactivation of S. Enteriditis and L. monocytogenes was apparent during the 8‐hr marination process, implying adaptation and resistance to low pH. Results suggest that salting or marinating of anchovy creates an environment in which pathogenic bacteria are inactivated. However, inherent resistance or possible adaptation to stresses can result to prolonged inactivation times; hence it is important to avoid contamination with high numbers of food‐borne pathogens. Practical applications Many food‐borne bacterial pathogens can survive at low pH and aw, especially in cases in which they might adapt to the imposed stresses and become resistant. Knowing the time required to reduce food‐borne pathogens is of great interest for ensuring safety of traditional seafood.