In a two-stage digestion system, also known as a multistage digestion system, multiple digestion containers are optimized to bring maximum control over the bacterial communities developing within the digester. As with single stage digestion, there are multiple types of bacterial processes. In the first reaction vessel, hydrolysis, acetogenesis and acidogenesis occur simultaneously. During this reaction feedstock is added and controlled. That organic material is then heated to the ideal operating temperature (either mesophilic or thermophilic) and then pumped into a methanogenic reactor. During this process, a sterilization process may also occur heating the matter to a temperature that kills the harmful bacteria found in waste.
Once these bacteria reactions have taken place, a residence time occurs which allows the feed bacterial to begin degrading and developing gases. This time ranges in most cases from 14 to 40 days depending on the type of feedstock and the digestion system utilized. In some cases, in an up flow anaerobic sludge blanket digestion system, a hydraulic residence time can be as short as even an hour with solid retention times can be up to 90 days. Continuous digesters utilize mechanical and hydraulic devices which continually mix the contents enabling the bacteria and the feed to be in contact with one another. This also allows for a more consistent volume within the digestion tanks as the excess material is continuously extracted.