In this paper we present a two-step micro continuous flow-through method for synthesizing colloidal dispersions of noble metal core/shell and multishell nanoparticles in aqueous solutions in the presence of cetyltrimethylammonium bromide (CTAB). The synthesis is based on the reduction of the metal salts HAuCl4 and AgNO3 at the surface of seed particles by ascorbic acid. In the micro fluidic system, constant residence times and an effective mixing were achieved by applying the segmented flow principle. The colloidal solutions were analyzed by differential centrifugal sedimentation, UV–vis spectrophotometry, and scanning electron microscopy. The size distribution of the Au/Ag core/shell and multishell nanoparticles synthesized by the micro flow-through technique was very narrow. In case of Au/Ag core/shell nanoparticles, an average diameter of 20nm with a distribution half width of 3.8 nm, and for Au/Ag/Au multishell nanoparticles an average diameter of 46nm with a distribution half width of 7.4nm were obtained. The optical spectra of the particle solutions exhibited drastic changes with the deposition of each additional metal shell. Due to the intense changes in their optical properties, the prepared particles are of interest for future sensing applications as well as for labelling in bioanalytics or as nonlinear optical devices. Furthermore, it is shown that micro reactors are well suited to control the synthesis of complexly structured Au/Ag multishell nanoparticles with a high homogeneity and an extremely narrow size distribution. Especially by applying a micro segmented flow, an improvement of the product quality is achieved because of a high internal segment mixing efficiency and a suppression of residence time distribution.