Iron oxide nanoparticles were synthesized using a vortex microfluidic system and subsequently functionalized with a primary shell of salicylic acid, recognized for its ability to increase the stability and biocompatibility of coated materials. In the second stage, the vortex platform was placed in a magnetic field to facilitate the growth and development of a porous silica shell. The selected drug for this study was micafungin, an antifungal agent well regarded for its effectiveness in combating fungal infections and identified as a priority compound by the World Health Organization (WHO). The resulting nanocomposite system was characterized using various techniques, including Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), transmission electron microscopy (TEM), dynamic light scattering (DLS), Brunauer–Emmett–Teller (BET) analysis, UV-Vis spectroscopy, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The synthesis method produced nanoparticles with dimensions of 5–7 nm, highlighting the advantages of the chosen approach. A desorption profile was established using a continuous-flow, UV-Vis analysis system, indicating that the bioactive compound was released slowly; after two hours, approximately 50% of the loaded micafungin was detected in the release medium. Furthermore, the results obtained from the FT-ICR MS analysis provided molecular-level confirmation, thereby supporting the release mechanism of micafungin from the nanosystem.