A microfluidic reactor for the synthesis of chitosan coated iron-oxide nanoparticles is described. Tapered double T-junction is used to generate droplets of reactants (iron chloride solution and chitosan solution) which were merged using a pillar array. Third reactant ammonia solution is introduced after the mixing of already merged droplets. Ammonia solution initiates the reaction and precipitates are collected at the outlet. Transmission electron microscope (TEM) imaging along with Fourier transform infrared spectroscopy (FTIR) is used to characterize the nanoparticles. These nanoparticles have applications in nano-medicine where they can be used as drug carriers.