Methane fermentation is an attractive practice in waste processing, which enables one to both control pollution and recover energy. This kind of anaerobic digestion is exposed to inhibitors, which can retard the process and cause failure. The mechanism causing toxicity of these substances and their impact on the efficiency of the process are already known, but there is still not much information about their influence on methane fermentation microorganisms' activity and the composition of microbiota. In this review, based on 168 articles, we present a summary of the up‐to‐date research on the inhibition of anaerobic processes by some specific toxicants: ammonia, sulfides, ions of light metals, heavy metals, antibiotics, ethylene and acetylene, chlorophenols, halogen aliphatic hydrocarbons, aliphatic nitro compounds, and long‐chain fatty acids. This review principally focuses on the impact of these inhibitors on the microorganisms involved in the process. More accurate recognition of methane fermentation inhibition mechanisms, with particular emphasis on the microbiological aspect, can help to improve the efficiency of the process.