Biotransformation of l-phenylalanine (l-1a) and five unnatural substrates (rac-1b–f) by phenylalanine ammonia-lyase (PAL) was investigated in a novel microfluidic device (Magne-Chip) that comprises microliter volume reaction cells filled with PAL-coated magnetic nanoparticles (MNPs). Experiments proved the excellent reproducibility of enzymecatalyzed biotransformation in the chip and the excellent reusability of the enzyme layer during 14 h continuous measurement (>98% over 7 repetitive measurements with l-1a). The platform also enabled fully automatic multiparameter measurements with a single biocatalyst loading of about 1 mg PAL-MNP. Computational fluid dynamics (CFD) calculations were used to study the flow field in the chambers and the effect of unintended bubble formation. Optimal flow rate for l-1a reaction and specific activities for rac-1b–f under these conditions were determined.