The aim of this study was to evaluate the effects of ultraviolet (UV) radiation (ultraviolet A (UVA), ultraviolet B (UVB) and ultraviolet C (UVC) at 30-90 J/m²) on the membrane properties of lactobacilli and bifidobacteria, and their bioconversion of isoflavones in prebiotic-soymilk. UV treatment caused membrane permeabilization and alteration at the acyl chain, polar head and interface region of membrane bilayers via lipid peroxidation. Such alteration subsequently led to decreased (p < 0.05) viability of lactobacilli and bifidobacteria immediately after the treatment. However, the effect was transient where cells treated with UV, particularly UVA, grew better in prebiotic-soymilk than the control upon fermentation at 37°C for 24 h (p < 0.05). In addition, UV treatment also increased (p < 0.05) the intracellular and extracellular β-glucosidase activity of lactobacilli and bifidobacteria. This was accompanied by an increased (p < 0.05) bioconversion of glucosides to bioactive aglycones in prebiotic-soymilk. Our present study illustrated that treatment of lactobacilli and bifidobacteria with UV could develop a fermented prebiotic-soymilk with enhanced bioactivity.