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Objective  Microbial analysis in milk preserved using heat-assisted Pulsed Electric Field (PEF) need to be assessed. In this study we analyze the microbial quality and virulence-associated genes in milk samples preserved using heat-assisted PEF from several producers in Indonesia.    Results  Milk samples were collected consisting of raw milk, milks taken after the heating, PEF, mixing, cooling, and packaging. Microbiological and Polymerase Chain Reaction (PCR) detection for virulence genes were performed. Heat-assisted PEF treatment gave 2.7–7.47 log reduction for TPC; 1.6–2.56 log reduction for MPN number; 3.13–6.48 log reduction for  S. aureus ; and for  B. cereus  there was an increase of 0.76 log and a reduction of 0.46 log. While milk samples from thermal pasteurization gave log reduction numbers of TPC, MPN, and  S. aureus  respectively 5.28; 2.56; and 4.73, for  B. cereus  was increasing 2.4 log. Producer C performed the best results with significant reduction compared with others (p < 0.005). There were no colonies of  L. monocytogenes  found in all of the samples. PCR results showed that milk samples possessed virulence genes 17.5% (10/57) of  invA  genes, 54.4% (31/57) of  nheA  genes, 68.4% (39/57) of  cytK  genes, 38.6% (22/57) of  nuc  genes, 63.2% (36/57) of  ileS  genes, while  hly  and  actA  genes were not detected.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13104-021-05805-3.

Microbial analysis and virulence genes detection of milk preserved using heat-assisted pulsed electric field