Microreactors made from cycloolefin copolymer (COC) were produced using the fused filament fabrication (FFF) method, which is a technology of additive manufacturing. The process began with a model designed in Autodesk Fusion 360 CAD program. Various microreactor systems were designed with different microchannel diameters, including 1000 μm, 800 μm, 500 μm, 300 μm and 200 μm. These systems were used for the synthesis of fatty acid methyl esters (FAME) i.e. biodiesel. Due to the small dimensions of the microchannels and the large interfacial surface, the microreactors provide fast mixing and satisfying temperature regulation in comparison to conventional process reactors. The choice of materials for the construction of microreactors is influenced by many factors. The most important being the type of chemical reaction carried out in the microreactor system, the behavior of the material due to the influence of solvents (or the compatibility of solvents and materials) and mechanical and optical requirements. The materials for the fabrication of the microreactor must be chemically inert and compatible with the fabrication protocol in order for the process to be carried out quickly, with minimal waste material. COC material met the listed criteria in previous studies and was therefore selected as the test material for this experiment. Chemical resistance of COC was determined by the degree of swelling. The results showed that the material was chemically resistant to polar solvents. When tested against nonpolar solvents, the chemical resistance of COC was reduced. Also, the actual diameter of the microchannel dimensions was determined after the reactors for the experiment were printed. According to the obtained results, there was a very slight deviation from the expected dimensions. After testing the properties of the polymer and the resolution of 3D printing, a batch reaction of biodiesel synthesis was performed. These results were used to make calibration diagrams from which the conversion of oil to biodiesel for the samples obtained from microreactor systems was calculated. Infrared spectrophotometric analysis showed that the reduction in microchannel diameter nor increase the retention time did not affect the increase in oil to biodiesel conversion for the cycloolefin copolymer. Gas chromatography confirmed the obtained results and provided more detailed data on the composition of biodiesel.