The controlled synthesis of nanoparticles (NPs) with stable crystal Structures and stable physical and chemical properties is a key issue for commercial applications. The use of a microfluidic reactor (MR) process has proven to be a flexible approach to control the fine crystal structures and the magnetic properties during the ripening and aging of the NPs . We have developed an in situ rapidly cooling microfluidic process (IRCMP) in which Co NPs with stable crystal structures and magnetic properties are synthesized by using elevated reaction temperatures followed by rapid quenching of the colloids to reduced temperatures. The Co NPs that are obtained by this process demonstrate stable crystal structures and stable magnetic properties for a much longer period of time (at least 3 months) than for Co NPs obtained by performing the reaction and the quenching processes at room temperature or under sonication.