Benzaldehyde lyase from Pseudomonas fluorescens Biovar I [BAL; E.C.4.1.2.38] catalyzes the stereoselective formation of C–C bonds coupling aldehydes to generate alpha-hydroxy ketones. A broad range of poorly water-soluble substrates are accepted in forward and reverse reactions. In this study, the stability of BAL in aqueous–organic biphasic systems as promising reaction media was systematically investigated using methyl-tert-butylether, 2-octanone, and toluene as the organic phase. Surprisingly, a strong individual molecular toxicity of these water-immiscible solvents was observed along with the interfacial toxicity exerted by the aqueous–organic interfaces. They could be considerably reduced by covalent attachment of methoxy-poly(ethylene) glycol (mPEG750 and mPEG2000) to the enzyme surface increasing the half-life by a factor of up to 18. However, under reactive conditions solvent effects were strongly superimposed by an additional deactivating effect, possibly caused by the aldehyde substrate, and no differences between unmodified and modified BAL were detectable. For technical application of the enzyme in aqueous–organic biphasic media additional strategies for stabilization will therefore be desirable.