Heavy metals affect the biochemical reactions that take place during anaerobic digestion processes of organic matter. In this review, the different effects observed in anaerobic digestion processes and during the production of biomethane and biohydrogen from several substrates contaminated with and/or inheriting heavy metals from the substrates themselves were discussed. It has been found that heavy metals exert important roles in biochemical reactions. Heavy metals like copper, nickel, zinc, cadmium, chromium and lead have been overwhelmingly reported to be inhibitory and under certain conditions toxic in biochemical reactions depending on their concentrations. Heavy metals like iron may also exhibit stimulatory effects, but these effects have been scantily observed. This review also concludes that the severity of heavy metal inhibition depends upon factors like metal concentration in a soluble, ionic form in the solution, type of metal species, and amount and distribution of biomass in the digester or chain of biochemical reactions which constitute the anaerobic digestion process. A majority of studies have demonstrated that the toxic effect of heavy metals like chromium, cadmium and nickel is attributable to a disruption of enzyme function and structure by binding of the metal ions with thiol and other groups on protein molecules or by replacing naturally occurring metals in enzyme prosthetic groups. This review has not found published data on the effects of heavy metals on the hydrolysis stage of anaerobic digestion process chemistry, and hence further studies are required to depict any changes.