The formation of stable emulsions in biphasic biotransformations catalyzed by microbial cells turned out to be a major hurdle for industrial implementation. Recently, a cost-effective and efficient downstream processing approach, using supercritical carbon dioxide (scCO(2)) for both irreversible emulsion destabilization (enabling complete phase separation within minutes of emulsion treatment) and product purification via extraction has been proposed by Brandenbusch et al. (2010). One of the key factors for a further development and scale-up of the approach is the understanding of the mechanism underlying scCO(2)-assisted phase separation. A systematic approach was applied within this work to investigate the various factors influencing phase separation during scCO(2) treatment (that is pressure, exposure of the cells to CO2, and changes of cell surface properties). It was shown that cell toxification and cell disrupture are not responsible for emulsion destabilization. Proteins from the aqueous phase partially adsorb to cells present at the aqueous-organic interface, causing hydrophobic cell surface characteristics, and thus contribute to emulsion stabilization. By investigating the change in cell-surface hydrophobicity of these cells during CO2 treatment, it was found that a combination of catastrophic phase inversion and desorption of proteins from the cell surface is responsible for irreversible scCO(2) mediated phase separation. These findings are essential for the definition of process windows for scCO(2)-assisted phase separation in biphasic whole-cell biocatalysis. Biotechnol. Bioeng. 2015;112: 2316-2323. (c) 2015 Wiley Periodicals, Inc.