A batch system is the simplest form of digestion. Biomass is added to the reactor at the start of the process in a batch and is sealed for the duration of the process. Batch reactors suffer from odor issues that can be a severe problem when they are emptied. Typically, biogas production will be formed with a normal distribution pattern over time. The operator can use this fact to determine when they believe the process of digestion of the organic matter has completed. As the batch digestion is simple and requires less equipment and lower levels of design work it is typically a cheaper form of digestion.

In continuous digestion processes organic matter is constantly added (contin­uous complete mixed) or added in stages to the reactor (continuous plug flow; first in-first out). Here the end products are constantly or periodically removed, resulting in constant production of biogas. Single or multiple digesters in sequence may be used. Examples of this form of anaerobic digestion include continuous stirred-tank reactors (CSTRs), upflow anaerobic sludge blanket (UASB), expanded granular sludge bed (EGSB) and internal circulation reactors (IC).