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). This type of automated cleaning makes the cleaning of vessels and pipework more effective and efficient. CIP systems can either be single use sets where fresh detergent solutions are used every clean or rinse recovery sets where the detergent solution is recovered to be used on a subsequent clean.  Pipework internals on CIP systems are cleaned by turbulent flow of the liquids along the pipework and vessels are cleaned by static or rotating spray heads in the vessel.

The external cleaning of fillers and conveyors across the process and packaging plant, in general, will be undertaken using a medium pressure washdown system to foam, rinse and disinfect them.

Conveyor systems in these plants also require lubrication, which can either be dry or aqueous based. The function of a lubricant is to allow the conveyor track to run freely under packages. Lubricants also provide detergency to wash away any spillages and lubrication of drive bearings. Some lubricants also contain biocidal properties to prevent slime growth.