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In this paper, novel magnetic silica nanocomposites were prepared by anchoring magnetite nanoparticles onto the outer surface of mesoporous SBA-15 silica; the magnetic nanoparticles were prepared by microemulsion and solvothermal methods, varying the synthesis conditions in order to control the final physicochemical, textural and magnetic properties. The morphology and mesostructure of the materials were characterized by X-ray diffraction (XRD), Fourier-Transform Infrared Spectroscopy (FTIR), N2 adsorption–desorption, and Transmission and Scanning Electron Microscopy (TEM and SEM). Magnetic silica nanocomposites feature a two-dimensional hexagonal arrangement constituted by a homogeneous pore channel system with diameters between 13 and 18 nm and a Brunauer–Emmett–Teller (BET) surface area higher than 260 m2 g−1. The different morphologies of the samples are given by the presence of diverse magnetic nanoparticle arrangements covalently linked onto the outer surface of the mesoporous silica rods. This confers on them a superparamagnetic behaviour with a magnetic response between 50–80 emu g−1, even though the weight percent of magnetite present in the samples does not exceed 21.7%. In addition, the magnetic nanocomposites exhibit magnetic hyperthermia with moderate Specific Absorption Rate (SAR) values