Through hydrolysis the complex organic molecules are broken down into simple sugars, amino acids, and fatty acids.  Acetate and hydrogen produced in the first stages can be used directly by methanogens. Other molecules such as volatile fatty acids (VFA’s) with a chain length that is greater than acetate must first be catabolised into compounds that can be directly utilised by methanogens.  The biological process of acidogenesis is where there is further breakdown of the remaining components by acidogenic (fermentative) bacteria. Here VFAs are created along with ammonia, carbon dioxide and hydrogen sulfide as well as other by-products.  The process of acidogenesis is similar to the way that milk sours.
The third stage anaerobic digestion is acetogenesis. Here simple molecules created through the acidogenesis phase are further digested by acetogens to produce largely acetic acid as well as carbon dioxide and hydrogen.  The terminal stage of anaerobic digestion is the biological process of methanogenesis. Here methanogens utilise the intermediate products of the preceding stages and convert them into methane, carbon dioxide and water. It is these components that makes up the majority of the biogas emitted from the system. Methanogenesis is sensitive to both high and low pHs and occurs between pH 6.5 and pH 8.[42] The remaining, non-digestable material which the microbes cannot feed upon, along with any dead bacterial remains constitutes the digestate.
A simplified generic chemical equation for the overall processes outlined above is as follows:

C₆H₁₂O₆ → 3CO₂ + 3CH₄

Process temperature affects the rate of digestion and is normally maintained in the mesophillic range (95 to 105 degrees Fahrenheit). It is possible to operate in the thermophillic range (135 to 145 degrees F), but this digestion process is less stable and must be closely monitored.