Organic compounds are catabolized by fermentation when sulfate, nitrate, or iron is absent from an anoxic environment. In Clostridial fermentation, the Clostridium species either ferments sugars or amino acids. In sugar fermentation, butyric acid, acetone, and butanol are produced. If butyrate is synthesized, extra ATP is produced and the organism with continue to prefer butyrate unless the environment becomes unfavorable. When acetone is produced, butanol can also result from the process. For every acetone molecule, two NADH produced in glycolysis are not reoxidized.

Proteolytic Clostridia can also ferment amino acids released from proteins of dead organisms. The amino acid is catabolized to yield fatty acid-CoAs which is used to produce ATP by substrate level phosphorylation. Additionally, amino acid fermentation can be coupled in a process called the Strickland reaction.

In syntrophy, two different organisms cooperate to degrade a substance that one organism could not do alone. Most syntrophic reactions involve secondary fermentation of the fermented products of other organisms. For example, the H2 produced by Pelotomaculum is used as an electron donor by a methanogen to produce methane in an exergonic reaction. Syntrophic bacteria are often key links in anoxic steps of the carbon cycle. Synthrophs use reduced fermentation products to release H2 which is important for anaerobic respiration. This circumvents the problem of running out of electron acceptors other than CO2.

In mixed-acid fermentation, a glucose molecule is converted into a variety of acids. It is an anaerobic process used by bacteria such as E. coli. The products of mixed-acid fermentation includes lactate, acetate, succinate, formate, ethanol, H2, and CO2. The product form depends on the bacteria and what enzymes they contain. This biological process is often valued by biotechnological industries for applications in biofuel.