Performance of food safety management system (FSMS) by Self diagnostic instrument (DI) and Microbial assessment scheme (MAS) are still new approaches in Vietnamese Pangasius processing industries. Performance variability of food safety management systems (FSMS) in practice during processing steps makes microbial quality and safety of Pangasius hypothalamus products very challenging. Therefore, 117 samples of fish, water and environment were collected throughout processing to assess the effective operation of the FSMS in practice. The dynamics and variations in the microbial quality and safety were observed. The microbial count of the final products ranged 6.8-7.7 log CFU/g of total mesophilic count, <1-<2 log CFU/g of Escherichia coli, <1-6.3 log CFU/g of Coliform and <2-4.6 log CFU/g of Staphylococcus aureus. High prevalence of pathogens was observed on processed fish; 15/36 Listeria monocytogenes and 1/36 Salmonella spp. with a similar trend in food contact surfaces, hands of operators and water. More attention should be focused on this company because the current FSMS is not performing effectively by means of Self-Diagnostic Instrument (DI) and Microbial Assessment Scheme (MAS) tools. These assessment tools are necessary to implement routinely to validate the FSMS in place.