A system and method for controlling bacteria in the production of whey protein concentrate (WPC) using an organic oxidizer. In embodiments, peracetic acid is introduced into whey solution before or after it encounters one or more ultrafilters. The peracetic acid, even when used in minute quantities, has proven to have sufficient antimicrobial effect such that bacteria counts in the filter are maintained at acceptable levels. The reduction in bacteria not only helps reduce WPC bacteria counts, but also enables the filters to run longer between cleanings.