This study aimed at utilizing electroporation to further enhance the growth of lactobacilli and their isoflavone bioconversion activities in biotin-supplemented soymilk. Strains of lactobacilli were treated with different pulsed electric field strength (2.5, 5.0 and 7.5 kV/cm) for 3, 3.5 and 4 ms prior to inoculation and fermentation in biotin-soymilk at 37°C for 24 h. Electroporation triggered structural changes within the cellular membrane of lactobacilli that caused lipid peroxidation (p < 0.05) and alteration of membrane fluidity (p < 0.05). This was due to the application of electric potential difference across membrane that induced pores formation and subsequently increased membrane permeability. Reversible permeabilized cells resumed growth to >9 log CFU/ml after fermentation in biotin-soymilk (p < 0.05). Lactobacilli cells treated at electric field strength of 7.5 kV/cm for 3.5 ms also showed enhanced β-glucosidase activity (p < 0.05) compared to lower doses and control, leading to increased bioconversion of isoflavones glucosides to aglycones in biotin-soymilk (p < 0.05). Results from this study show that electroporation could be used to produce biotin-soymilk with increased bioactive aglycones.