The aim of this study was to prepare microparticles based on chitosan-copper(II) ion complex (CHT-Cu) using a de novo microreactor. By manipulating the flow rates of the continuous and dispersed phases, the goal was to achieve a narrow size distribution of the CHT-Cu microparticles. In the experimental part of this study, a poly(methyl-methacrylate) (PMMA) microreactor with T-junction geometry and channels of diameter 940 ± 50 μm was prepared by surface machining technique using a milling machine. The dispersed phase was CHT-Cu complex solution, while the continuous phase was sunflower oil with or without an emulsifier (SPAN 85). The study examined the effects of varying the flow rates of the continuous and dispersed phases, as well as using different compositions of the neutralizing medium. The neutralizing medium was a 1.25 mol dm^-3 sodium hydroxide (NaOH) solution or a mixture of NaOH solution and 96 vol. % ethanol (volume ratio 1:1). Additionally, different modifications of the microreactor were tested, such as the use of a metal needle and a tube (pipe) for easier removal of the product (solution) from the microreactor’s outlet, and the use of a Teflon layer on the microreactor’s surface, on the size and shape of the resulting CHT-Cu microparticles. The obtained CHT-Cu microparticles were of average width 567 ± 190 μm and length 1091 ± 250 μm, regardless of the applied flow rates of the continuous and dispersed phases, but varied in shape due to the use of different compositions of the neutralizing medium. During washing and drying, the resulting microparticles decreased in size while retaining an irregular, elongated shape and the formation of agglomerates. Fourier-transform infrared spectroscopy (ATR-FTIR) indicated the presence of electrostatic forces between the metal ions and the chitosan polymer chain without the appearance of new absorption bands, confirming the success of the applied washing and drying procedures. CHT-Cu microparticles obtained using 1,25 mol dm^-3 NaOH and 96 vol.% EtOH as a neutralization medium, with continuous and dispersed phase flow rates of 50 and 0,5 mL h^-1 proved to be a promising system. The results of this study indicate the potential use of microreactors for obtaining microparticles based on chitosan and metal ions, which can serve as a basis for further research aimed at optimizing the process to produce micro-particles with more regular shapes and narrower size distribution, for the development of targeted drug delivery systems.