Magnetite nanoparticles (FeO NPs) are among the most investigated nanomaterials, being recognized for their biocompatibility, versatility, and strong magnetic properties. Given that their applicability depends on their dimensions, crystal morphology, and surface chemistry, FeO NPs must be synthesized in a controlled, simple, and reproducible manner. Since conventional methods often lack tight control over reaction parameters and produce materials with unreliable characteristics, increased scientific interest has been directed to microfluidic techniques. In this context, the present paper describes the development of an innovative 3D microfluidic platform suitable for synthesizing uniform FeO NPs with fine-tuned properties. On-chip co-precipitation was performed, followed by microwave-assisted silanization. The obtained nanoparticles were characterized from the compositional and microstructural perspectives by X-ray diffraction (XRD) and transmission electron microscopy (TEM). Moreover, supplementary physicochemical investigations, such as Fourier Transform Infrared Spectroscopy (FT-IR), Kaiser Test, Ultraviolet-Visible (UV-Vis) Spectrophotometry, Dynamic Light Scattering (DLS), and Thermogravimetry and Differential Scanning Calorimetry (TG-DSC) analyses, demonstrated the successful surface modification. Considering the positive results, the presented synthesis and functionalization method represents a fast, reliable, and effective alternative for producing tailored magnetic nanoparticles.