In the present work, gold based catalysts were synthesized and immobilized on the surface of cyclic olefin copolymer (COC) microreactors. The microreactors were subsequently applied in a homemade microfluidic system for synthesizing benzaldehyde by oxidation of benzyl alcohol in water medium. The Au nanoparticles (NPs) immobilized on the inner surface of the microchannel showed a very high selectivity (94%) for benzaldehyde, while zeolite NPs exhibited only an adsorption feature to this reaction. Moreover, the results showed that the AuNP catalytic activity was maintained for at least 9 hours. However, the obtained conversion with AuNPs was only 20%, indicating a relatively low productivity. In comparison, AuNPs assembled on the surface of zeolite NPs (AuNPs@zeolite) and immobilized in the microchannel showed the best catalytic performance, as the highest benzaldehyde selectivity (>99%) with a relatively high benzyl alcohol conversion of 42.4% was achieved under the same conditions. To the best of our knowledge, this is the first example demonstrating the use of AuNP or AuNP@zeolite catalysts in a microsystem performing such high selectivity for benzaldehyde in water medium.