Abstract Although whole-cell biocatalysis, as well as microreactor technology, are gaining importance in modern biotechnology, there are just a few literature reports on whole-cell biocatalysis in microreactors. In the present work, a continuously operated microreactor with permeabilized Saccharomyces cerevisiae cells was made out of commercially available plastic tubes and tested as a tool for the development of l -malic acid production accomplished by hydration of fumaric acid. Cells were immobilized on inner walls of microchannels by means of 3-aminopropyltriethoxysilane and glutaraldehyde and further permeabilized in order to enhance mass transfer across the membrane. The effects of different process parameters including medium pH, substrate inlet concentration and flow rate, cell permeabilization conditions, as well as catalyst stability were evaluated and the results compared to previously published data obtained within a bench-scale bioreactor. The presented microfluidic device with immobilized biocatalyst built from low cost and disposable materials could be applied for the fast development of other whole-cell biotransformations.