Magnetic nanoparticles (MNPs) sharing heterojunctions with other magnetic, plasmonic, or semiconductor nanodomains form a large family of inorganic hybrid nanostructures of high interest due to their synergistic properties and multitasking performance in highly demanding technological fields. This chapter provides an updated review of the strategies mostly used for the synthesis of multifunctional bi-magnetic, magneto-plasmonic, and magneto-semiconductor hybrid nanostructures and the advances they represent. In the subsequent sections, the most recent (mainly within the last five years) and promising examples of the application of magnetic-based hybrid nanostructures are described and organized by their field of application, including multimodal therapy for biomedicine, magnetically assisted catalysis for energy production, and pollutant detection and removal for environmental remediation. Finally, some conclusions and perspectives are outlined in an attempt to foresee the future utilization of magnetic-based inorganic hybrid nanostructures.