Microreactors have attracted wide attention in the nano-and biotechnology field because they offer many advantages over standard liquid phase reactions. We report the development of a magnetic microreactor for reliable, fast and efficient surface functionalization of superparamagnetic iron oxide nanoparticles (SPIONs). A comprehensive study is described of the development process in terms of setup, loading capacity and efficiency. We have performed experimental and computational studies in order to evaluate the trapping efficiencies, maximum loading capacity and magnetic alignment of the nanoparticles. The results show that capacity and trapping efficiencies are directly related to the flow rate, elution time and reactor type. Based on our results and the developed magnetic microreactor, we describe a model multistep surface derivatization procedure of SPIONs.