The surface modification of various nanoparticles with silica has been exploited to increase their utility for bioapplications. However, silica encapsulation through conventional methods requires long reaction times (hours to days). Herein, we demonstrated that uniform and spherical silica encapsulation of magnetic nanoparticles can be achieved within 10 min via microwave irradiation after phase transferring monodisperse magnetic nanoparticles from organic to water phase. In addition, we showed that silica shell addition through microwave synthesis is more effective than conventional heating methods, such as a hot plate. The approach that we propose may be useful in preparing multifunctional nano-probes, particularly for radiolabeling, which requires fast preparation times.