The use of ionic liquids (ILs) as nonconventional reaction media in enzyme catalyzation has gained increasing attention for developing green chemical processes because of the physical and chemical characteristics of ILs. Some have been shown to be by far the best nonaqueous media for enzyme-catalyzed reactions, because the enzymes display a high level of activity and stereoselectivity in synthesizing many different substrates, as well as by their excellent ability to stabilize enzymes toward re-use. The different operational strategies used for enzymatic processes in ILs are analyzed. Protocols to synthesize different fine chemical products, such as aspartame, butyl butyrate, R-2-pentyl propionate, Nacetyllactosamine, and polyester are described in detail, including analytical techniques. A detailed description of the procedure for recovering and cleaning of ILs to be re-used is also included, as well as notes containing special cautions.