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Being considered greener alternatives to ionic liquids (IL), deep eutectic solvents (DES) and natural deep eutectic solvents (NADES) have currently attracted broad interests from academics and industry. In this study, the transformation of isoeugenol to vanillin catalyzed by Lysinibacillus fusiformis CGMCC1347 cells was taken as the model reaction to examine the impacts of 24 DESs and 21 NADESs as cosolvents on whole-cell biocatalysis. Both types of cosolvents showed the ability of improving the production yields up to 142% and 132% of the ones obtained in (NA)­DES-free aqueous systems, respectively. The data obtained by confocal laser scanning microscopy and flow cytometry tests and measurements of OD260 and OD280 agreed well with the bioconversion data, suggesting that addition of these cosolvents may be beneficial to whole-cell biocatalysis in enhancing the cellular membrane permeability. Interaction of DES with bacterial cell wall was discussed. The cells immobilized in PVA-alginate beads granted an augmented production yield in the presence of DES and NADES, up to 181% of the one obtained in a pure water system, and their catalytic activity was well maintained after being used for at least 13 cycles.