© 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.Nanostructures are capable of major changes in our life. However, the game changing properties of experimental nanostructures mostly are not repeatable for the industry and it is not easy to produce the amount of nanoparticles necessary for the industrial world. Repeatable methods, which do not require highly trained personnel, for industrial-scale production should be developed to transfer the academic research to the use of people. Although there are various successful microfluidics devices that have been designed for microstructures synthesis, the synthesis of the nanostructures is not an enlightened area and there is a need for research to reach a better state. Especially, the development and design of microfluidics devices for biopolymeric nanoparticles are very important. The biopolymeric nanoparticles have uses in both nanotechnology and nanomedicine especially as theragnostic tools. In this study, a microfluidic device has been modeled, designed, and manufactured for especially iron oxide core chitosan nanoparticles. The microfluidics channels were manufactured by 3D printing. After nanoparticles synthesized by manufactured device, these particles were characterized, and their properties were examined. In addition to the flow rate, chemical concentrations, and pH, the structure of the microfluidics channel and hurdles have effects on the particle size and particle size distribution. Best results were obtained with 120-120ml/h flow rates and 0.06-0.03% concentrations at pH 4.5 for chitosan-tripolyphosphate couple. The nanoparticles that were produced in microchannels with hurdles under these conditions have a DLS measurement of 190±15 nm in diameter with 69% intensity. In conclusion, the 3D printed microfluidic channels are able to synthesize nanoparticles in a reproducible way with or without iron oxide core.