Ionic liquids (ILs) have been widely recognized as environmentally benign solvents. Their unique properties, including negligible vapor pressure, non-flammability, a wide liquid range and their tunable physicochemical properties by proper selection of cations and anions, make them attractive green solvents in a variety of fields such as organic synthesis/catalysis, extraction/ separation, and electrochemistry, amongst others. In this paper, the recent technological developments and their prospects in the application of ILs in microbiology and biochemical engineering, including enzymatic reactions, protein folding/refolding and biomass dissolution, are discussed.