Room-temperature ionic liquids (ILs) represent molten salts entirely consisting of ions, usually a charge-stabilized organic cation and an inorganic or organic anion. ILs are liquids at ambient temperature but possess characteristics unusual for the common liquid solvents, such as negligible vapor pressure, high thermal stability and most over the ability to mix and match libraries of cations and anions in order to acquire desirable physical and chemical properties . The opportunity to obtain tunable density, viscosity, polarity and miscibility with common molecular liquids gave rise to a variety of applications of the ILs  as environmentally benign solvents, extractants or auxiliaries. In particular, numbers of innovations in the methods for recovery and purification of biologically derived compounds involve ILs used solo or partnered with other liquids in biphasic systems [3,4,5]. It should be noted that the ILs are not intrinsically greener than the traditional solvents, given that their production is usually more resource-demanding, but the inherent potential for recycling and reuse, and for prevention of chemical accidents gives the ILs advantages ahead. The present chapter provides a state-of-the-art overview on the basic applications of the ILs in biphasic systems aimed at downstream processing of valuable fermentative products, enzymes and organic acids. Main industrially important enzymes, lipases and carbohydrases, are considered and a description of the IL-assisted aqueous biphasic systems (ABS) and the results obtained in view of enzyme yield and purity is made. ILs serve different functions in the ABS, main phase-segregating constituents (mostly in the IL/salt ABS) or adjuvants to the polymer/salt ABS. Enzyme isolation from the contaminant proteins present in the feedstock can be carried out either in the IL-rich or in the salt-rich phase of the ABS and for the reader’s convenience the two options are described separately. Discussion on the factors and parameters affecting the enzyme partitioning in the ABS with ILs guides the reader through the ways by which the interactions between the IL and the enzyme can be manipulated in favor of the enzyme purification through the choice of the ABS composition (IL, salt, pH) and the role of the water content and the IL-rich phase structure. The second part of the chapter is dedicated to the recovery of fermentative organic acids. Mostly hydrophobic ILs have been engaged in the studies and the biphasic systems thereof are summarized. The systems are evaluated by the extraction efficiency and partition coefficient obtained. Factors and parameters affecting the extraction of organic acids by ILs are highlighted in a way to unravel the extraction mechanism. The choice of IL and pH determines the reactive mechanism and the ion exchange, while the water content and the IL phase structure play roles in physical extraction. Procedures undertaken to enhance the efficiency and to intensify the process of extraction are also looked over. Finally, the experimental holes that need fill up in the future studies are marked. According to the author’s opinion an intense research with hydrophobic ILs is suggested as these ILs have been proved milder to the biological structures (both the microbial producer and the enzyme product), more effective in the organic acid recovery and suitable to perform “in situ” extraction. Extractive fermentation entails validation of ecological and toxicological characteristics of the ILs. The protocols for re-extraction of fermentative products separated by IL-assisted biphasic systems should be clearly settled along with the methods for ILs recycling and reuse. Novel more flexible approaches to process intensification can be implemented in order to adopt the separation by biphasic systems for use in industry.