Mixing with air and microorganisms in the environment during processing, unheated juice is subject to rapid microbial, enzymatic, chemical and physical deterioration. The low pH of most juices favours organisms such as yeasts, which have the potential to rapidly initiate fermentation. Unpasteurised juice has also been implicated in outbreaks of as E.coli O157 H7.

Most of the cleaning associated with a juice plant will involve cleaning in place (CIP) pipework, pumps, tanks and fillers whilst external cleaning of fillers, conveyors across the process and packaging plant in general will be done using a medium pressure washdown system to foam, rinse and disinfect them thoroughly. Conveyor systems in these plants also require lubrication, which can either be dry or aqueous based.