The aims of this study were to verify compliance with cleaning and disinfection protocols in 16 fish stores of local markets in Ibagué, Tolima, Colombia, according to current regulations by means of a checklist, and to evaluate surfaces, utensils, and water that come into direct contact with fish by luminometric tests. The presence or absence of pathogenic microorganisms in fish, e.g., Escherichia coli O157:H7 and Salmonella spp., was also determined using a 3M molecular detection system. Finally, the microbial loads of quality and safety indicator microorganisms (E. coli and/or coliforms, aerobic mesophilic bacteria, Enterobacteriaceae, and Staphylococcus aureus) were evaluated with Petrifilm plates. Responses to the checklist showed weaknesses in good manufacturing practices. Luminometry results revealed that 77.2% of the surfaces, 76.9% of the utensils, and 43.7% of water samples met the established rejection limit (more than 600 relative light units). Additionally, although the absence of E. coli O157:H7 and Salmonella spp. was noted, there was a high load of E. coli and/or coliforms, i.e., microorganisms that indicate that the sanitation conditions at the evaluated fish stores posed potential food safety problems. These findings necessitate corrective measures to guarantee quality of the final product. HIGHLIGHTS