Although the farming of Pangasianodon hypophthalmus is of worldwide economic importance, only little scientific information is currently present on the microbiological quality and safety of these fish fillets throughout the processing chain. This research assessed the microbiological quality and safety of P. hypophthalmus in a Vietnamese Pangasianodon processing company as a case study. The company was initially characterized by a diagnosis of the food safety management system (FSMS) performance by an in-depth interview, which is referred to as a diagnostic instrument. Secondly, a microbiological assessment scheme (MAS), an active and repetitive sampling methodology, was used to evaluate the food safety output and the microbiological quality from raw material until final product. The overall MAS result (level 2) was found to be slightly lower than the company?s food safety performance indicators had indicated (level 2?3). It can be concluded that the microbiological risk of the Vietnamese company and its products is medium high. This is mainly due to the lack of data and knowledge regarding the origin and composition of the microbiological flora present in the fish and in the processing environment. The variability in concentrations of microorganisms also contributed to this lower MAS score and could probably be reduced by improving some specific aspects of the FSMS and the production process.