The surface and catalytic properties of natural magnetite were modified using plasma treatment, and were characterized using X-ray diffraction, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, N2 adsorption–desorption, and scanning electron microscopy. The results show the production of nanostructured magnetite, from its natural particles, with an average diameter in the range of 20–40 nm. The application of nanostructured magnetite in a heterogeneous Fenton process was investigated in the degradation of Basic Blue 3 (BB3) as a model pollutant in aqueous solution. The effects of operational parameters were studied with respect to decolorization efficiency. The application of a nanostructured magnetite catalyst allows the Fenton process to be operated at milder pH conditions (a pH of 5). A decolorization efficiency of 96% in the presence of plasma-treated magnetite was approximately two times higher than that of untreated magnetite. Negligible iron leaching and a simple separation of used catalyst using an external magnetite field are merits of using plasma-treated magnetite in heterogeneous Fenton process.