This study aimed at giving insight into microbiological safety output of a Hazard Analysis Critical Control Point (HACCP)-based Food Safety Management System (FSMS) of a Nile perch exporting company by using a combined assessment, FSMS-diagnosis and actual microbiological assessment. The FSMS diagnosis indicated FSMS activities at an average level operating in moderate-risk context level but with good system output. Likewise, microbiological assessment revealed a better system output with respect to pathogens (Vibrio cholerae, Listeria monocytogenes and Salmonella spp.) and faecal hygiene (Escherichia coli) as none of these were detected in any critical sampling location throughout the study. Although indicators of general process hygiene (that is, Enterobacteriaceae and TVC) exceeded regulatory limits and guidelines in raw materials and food contact materials, Staphylococcus aureus on operator's hands were beyond the general microbiological guidelines in the fish industry. Higher contamination levels of general process hygiene and personal hygiene indicators call for improvement on hygienic design, specific production and sanitation procedures, independent validation, process automation, and change in personnel recruitment criteria.