Microwave plasma heat treatment of iron oxide nanoparticles coated with conductive polymers (e.g.polypyrrole) is a simple method to produce highly electrically-conductive, magnetic nanoparticles, as the heat treatment induces conversion of the amorphous conductive polymeric material to a significantly more electrically-conductive graphitic structure. However, an undesirable side effect of such heat treatment is the decrease of magnetization of the iron oxide cores due to conversion to a non-magnetic phase. We report a facile route for rapid heat treatment of bare particles, silica coated, and silane coated iron oxide nanoparticlesvia plasma heating using a standard microwave oven. The initial phase of the iron oxide was maghemite (γ-Fe2O3) with a specific saturation magnetization (σs) of 75 emu/g. Upon microwave heat treatment, the magnetization was reduced to 6 emu/g as they were converted almost entirely to hematite (α-Fe2O3) phase. Silica coated maghemite with σs of 48 emu/g was reduced to magnetite (Fe3O4) and fayalite (Fe2SiO4) with a σs value of 34 emu/g. When the maghemite nanoparticles were coated with thin silane layers, the magnetization value increased to 86 emu/g after microwave treatment as the cores were converted to magnetite. The proposed method can thus be used to increase the crystallinity of the magnetic composites via rapid heat treatment, whilst preventing any adverse effects on magnetic properties.