The search for new compounds obtained by enzymatic synthesis with biological activities has increased in recent years. Therefore, we propose the optimization of the enzymatic synthesis of eugenyl isobutyrate in a packed-bed microreactor using the strategy of experimental design. The results have shown maximum conversion of 77% using flow rate of 8 μL min-1, eugenol to isobutyric anhydride molar ratio of 1:5 and temperature of 68 °C, thus showing the great potential of the continuous flow enzymatic synthesis for the production of compounds with bioactive properties. The lipase Novozym 435 has been proven to be a very efficient biocatalyst for the flow-mode production of eugenyl isobutyrate. In conclusion, we have designed and optimized a completely new, green bioprocess for the continuous synthesis of eugenyl isobutyrate.