Biocatalyst inactivation is caused by external stresses, including high pressures and temperatures, extreme pH's, organic media, freezing, drying, and oxidative, chelating, and denaturing agents. These stresses may result either in reversible or irreversible activity loss. The main structural and covalent mechanisms in biocatalyst inactivation such as the disulfide intra‐ and interexchanges, the deamidation of asparagine residues, the decomposition of disulfide bridges by β‐elimination, the hydrolysis of peptide chains, the β‐isomerization of asparagine and aspartic acid residues, and amino acid racemization are discussed. The strategies that have been developed to prevent biocatalyst inactivation, i.e. chemical modification immobilization, protein engineering, directed evolution, are briefly presented.