Aerogels have gained much interest in the last decades due to their specific properties, such as high porosity, high surface area, and low density, which have caused them to be used in multiple and varied fields. As the applicability of aerogels is tightly correlated to their morpho-structural features, special consideration must be allocated to the fabrication method. An emerging technique for producing nanostructured materials with tailored morphology and dimensions is represented by continuous-flow microfluidics. In this context, this work explores the synergic combination of aerogel-based materials with microfluidic synthesis platforms to generate advanced nanocomposite adsorbents for water decontamination. Specifically, this study presents the novel synthesis of a magnetic silica-based aerogel using a custom-designed 3D microfluidic platform, offering enhanced control over nanoparticle incorporation and gelation compared to conventional sol-gel techniques. The resulting gel was further dried via supercritical CO extraction to preserve its unique nanostructure. The multi-faceted physicochemical investigations (XRD, DLS, FT-IR, RAMAN, SEM, and TEM) confirmed the material's uniform morphology, high porosity, and surface functionalization. The HR-MS FT-ICR analysis has also demonstrated the advanced material's adsorption capacity for various pesticides, suggesting its adequacy for further environmental applications. An exceptional 93.7% extraction efficiency was registered for triazophos, underscoring the potential of microfluidic synthesis approaches in engineering advanced, eco-friendly adsorbent materials for water decontamination of relevant organic pollutants.