Scope: Whey protein isolate (WPI) contains vitamin B-12 and folate. However, the efficacy of WPI as a bioavailable source of these vitamins in the elderly with low vitamin B-12 was not previously tested. We investigated the effects of WPI supplementation on vitamin B-12 and folate status in blood and measured changes in homocysteine (HCY), methylmalonic acid (MMA), and genome integrity biomarkers in elderly individuals with low vitamin B-12 status. The effect of WPI was compared to soy protein isolate (SPI). Methods and results: In this randomized controlled cross-over intervention trial, 56 subclinically vitamin B-12-deficient participants received 50 g WPI or 50 g SPI as a control for 8 wk followed by 16-wk washout phase and then cross-over to alternative supplement for next 8 wk. Consumption of WPI resulted in significant increase in serum active B-12 (p < 0.0001) and serum folate (p = 0.0094). MMA, HCY, and nucleoplasmic bridges increased significantly after SPI intake but not after WPI (p = 0.052; p = 0.028; p = 0.0009, respectively). Conclusion: Results indicate that WPI consumption improves active B-12 and folate status. Unlike SPI, WPI consumption may prevent increase in MMA, HCY, and genome instability in older Australians with low vitamin B-12 status.