Despite the prevalence of fluorination reactions of organic compounds in the pharmaceutical industry, these reactions still encounter several problems such as low selectivity, yield, high demand on safety operational process and low sustainability. Introduction of fluorine into drug molecules increases the drug’s lipophilicity, improves its stability and pharmacokinetic properties. Thus, the fluorination chemistry is of great importance in a pharmaceutical industry. This project is focusing on fluorination and trifluoromethylation of functionalized piperidines, organic compounds with several biological and therapeutic properties. We propose a cutting-edge interdisciplinary approach to make the fluorination reactions more sustainable, safe and to increase the reaction yield, by transferring electrochemical fluorination reaction into a flow microreactor. Advantage of electrochemical reactions is that the side products are minimized as no chemical reagents are necessary. The main advantages of microreactors are excellent heat and mass transfer properties and high surface to volume ratio. The precise control of the temperature profile in the reactor and the residence time enhances process safety and leads to high reaction selectivity. An electrochemical flow microreactor will be developed and optimized for fluorination reactions of piperidines. Collaboration of organic chemist and chemical engineers is upmost importance to succeed in this interdisciplinary project connecting organic chemistry, flow technology and microreactor engineering. Proposed innovation will show a new specific application of electrochemical microreactor. This is an important step in electrification of chemical and pharmaceutical industry which leads to overall higher sustainability of the chemical production. In addition, by overcoming above mentioned problems with fluorination reactions in the batch, we will demonstrate that microreactors have a valuable place in the chemical industry.