This study aimed to evaluate the effects of electroporation on growth, bioconversion of isoflavones, and probiotic properties of parent organisms and subsequent passages of Bifidobacterium longum FTDC 8643. Electroporation with the strength of electric field at 7.5 kV cm(-1) for 3.5 ms was applied on B. longum FTDC 8643. The viability of B. longum FTDC 8643 increased significantly upon treatment with electroporation. Such treatment also enhanced the intracellular and extracellular beta-glucosidase activity, leading to enhanced production of bioactive isoflavone aglycones in mannitol-soymilk (P < 0.05). In addition, these treated cells also exhibited better tolerance toward acidic (pH 2 and pH 3) and intestinal bile salt condition compared to the control (P < 0.05). The electroporated cell also possessed better adhesion ability and antimicrobial activity (P < 0.05). However, all these positive effects were only prevalent in the parent cells and were not observed in their subsequent passages of electroporated cells. Our results suggested that electroporation could enhance the bioactive and probiotic potentials of parent cells of B. longum FTDC 8643 and could be used in the production of probiotic foods with enhanced bioactivity.