Deuterated compounds are important in drug discovery and development, e.g., to prepare the so-called stable isotopically labeled internal standards. However, their preparation can be challenging, and its scalability could be difficult with regard to safety aspects. Herein, we report the first continuous-flow iridium(I)-catalyzed ortho-directed hydrogen–deuterium exchange reaction in microreactors. An immobilized iridium(I) catalyst was loaded in continuous-flow microreactors, such as continuous stirred tank reactors and packed-bed reactors. Best results were obtained in a packed-bed reactor allowing deuterium labeling up to M +7.