The recent needs in the nanosciences field have promoted the interest towards the development of miniaturized and highly integrated devices able to improve and automate the current processes associated with efficient nanomaterials production. Herein, a green tape based microfluidic system to perform high temperature controlled synthetic reactions of nanocrystals is presented. The device, which integrates both the microfluidics and a thermally controlled platform, was applied to the automated and continuous synthesis of CdSe quantum dots. Since temperature can be accurately regulated as required, size-controlled and reproducible quantum dots could be obtained by regulating this parameter and the molar ratio of precursors. The obtained nanocrystals were characterized by UV-vis and fluorescence spectrophotometry. The band width of the emission peaks obtained indicates a narrow size distribution of the nanocrystals, which confirms the uniform temperature profile applied for each synthetic process, being the optimum temperature at 270 °C (full width at half maximum = 40 nm). This approach allows a temperature controlled, easy, low cost and automated method to produce quantum dots in organic media, enhancing its application from laboratory-scale to pilot-line scale processes.