This study's main objective was to fabricate an innovative three-dimensional microfluidic platform suitable for well-controlled chemical syntheses required for producing fine-tuned nanostructured materials. This work proposes using vortex mixing principles confined within a 3D multilayered microreactor to synthesize magnetic core-shell nanoparticles with tailored dimensions and polydispersity. The newly designed microfluidic platform allowed the simultaneous obtainment of FeO cores and their functionalization with a salicylic acid shell in a short reaction time and under a high flow rate. Synthesis optimization was also performed, employing the variation in the reagents ratio to highlight the concentration domains in which magnetite is mainly produced, the formation of nanoparticles with different diameters and low polydispersity, and the stability of colloidal dispersions in water. The obtained materials were further characterized by X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy, dynamic light scattering (DLS), and transmission electron microscopy (TEM), with the experimental results confirming the production of salicylic acid-functionalized iron oxide (FeO-SA) nanoparticles adapted for different further applications.