The choice of the optimal enzyme immobilization technique is extremely important for the application of enzyme technology in industrial production, where long-term stability under operating conditions is expected from the reaction catalysts. In addition to the use of biocatalysts, flow and microreactor technologies are increasingly being used in industrial processes, which enable, among others, the rapid development of processes in a timely and reactant efficient manner, while ensuring high productivity and extremely good process control due to the efficient heat and mass transfer. In order to immobilize the amine transaminase enzyme into the microreactor, various immobilization techniques were tested and compared with each other: covalent binding of the enzyme to nanomats and glutaraldehyde-treated nanomats, entrapment into alginate hydrogel, and cross-linking of enzyme aggregates. Immobilization by covalent binding of the enzyme to nanomats and glutaraldehyde-treated nanomats has proven to be inappropriate due to loss of enzyme activity. Entrapment of the enzyme into the alginate hydrogel resulted in its leaching from the polymer matrix, which also made this technique inappropriate. The most effective immobilization technique was the formation of cross-linked enzyme aggregates, which successfully immobilized the enzyme and ensured its continued use in the micro-flow system.