Two probiotic strains, Bifidobacterium animalis A and B, were used for the biotransformation of isoflavone glycosides in soymilk prepared from soy protein isolate (SPI) supplemented with skim milk powder (SMP) (SSMP). Unsupplemented soymilk (USM) and reconstituted skim milk powder (RSMP) were used as controls. The numbers of viable microorganisms in these products were enumerated. Lactose and isoflavone contents were quantified using high-performance liquid chromatography (HPLC). Our results showed that there was significantly higher biotransformation of isoflavone glycosides to aglycones in SSMP than that in USM. The levels of biotransformation were 83.96% and 85.43% for B. animalis A and B, respectively, compared to 74.30% and 72.82% for the USM. In addition, lactose utilization by both strains in SSMP was also higher than that in RSMP. At 24 h, 21.16 mg/mL of lactose was utilized in SSMP by B. animalis A compared with that of 16.88 mg/mL in RSMP. Consequently, the pH of SSMP was lower (3.80) than RSMP (4.00). However, the number of viable bacteria in SSMP was slightly lower than that in RSMP but significantly higher than that in USM. It appears that SMP enhanced the biotransformation of isoflavone glycosides to aglycones and SPI increased the lactose utilization by B. animalis A and B.