Methods for reducing thermophilic spore-forming bacteria that can lead to off-odors and tastes in beverage products, especially fruit or vegetable juice products, are provided. The methods employ one or more peroxy acids that are added to the beverage handling system prior to pasteurization and concentration of the beverage product. Particularly, the peroxy acid is added prior to final filtration of the beverage product upstream of the pasteurizer and concentrator.
