The investigation of stereoselective biocatalytic transformations at a single-cell level is to date an unsolved challenge. Here, we report the development of an integrated microfluidic device which enables the analytical characterization of enantioselective reactions at nanoliter scale by combining whole-cell catalyzed on-chip syntheses, chiral microchip electrophoresis, and label-free detection of enantiomers by deep UV time-resolved fluorescence. Using Escherichia coli expressing recombinant Aspergillus niger epoxide hydrolase as the model enzyme for various enantioselective reactions, we evaluated the approach for downscaling the reaction to a few hundred cells. Our work is thus an important step toward the analysis of single-cell stereoselective biocatalysis.