The interconnection of nanotechnology and medicine could lead to improved materials, offering a better quality of life and new opportunities for biomedical applications, moving from research to clinical applications. Magnetite nanoparticles are interesting magnetic nanomaterials because of the property-depending methods chosen for their synthesis. Magnetite nanoparticles can be coated with various materials, resulting in “core/shell” magnetic structures with tunable properties. To synthesize promising materials with promising implications for biomedical applications, the researchers functionalized magnetite nanoparticles with silica and, thanks to the presence of silanol groups, the functionality, biocompatibility, and hydrophilicity were improved. This review highlights the most important synthesis methods for silica-coated with magnetite nanoparticles. From the presented methods, the most used was the Stöber method; there are also other syntheses presented in the review, such as co-precipitation, sol-gel, thermal decomposition, and the hydrothermal method. The second part of the review presents the main applications of magnetite-silica core/shell nanostructures. Magnetite-silica core/shell nanostructures have promising biomedical applications in magnetic resonance imaging (MRI) as a contrast agent, hyperthermia, drug delivery systems, and selective cancer therapy but also in developing magnetic micro devices.