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Hybrid magnetite/maghemite nanoparticles (MNP) coated with waste-sourced bio-based substances (BBS) were synthesized and studied for the degradation of phenol, chosen as a model pollutant, in water. A systematic study was undertaken in order to rationalize MNP-BBS behavior and optimize their performance. The effect of experimental parameters, such as light irradiation, addition of hydrogen peroxide, and the ratio between hydrogen peroxide and MNP-BBS concentrations, was studied. The generation of hydroxyl radicals was assessed, and the recovery and re-cycle of the material was investigated. Our results indicate that phenol degradation could be attained by both Fenton and photo-Fenton processes, with higher efficiency in dark condition and in the presence of a suitable amount of hydrogen peroxide. Evidence was obtained for the roles of iron ions leached from the materials as well as of organic matter released in the solution upon partial photodegradation of the organic coating. The reusability tests indicated a lower but still valid performance of the material. Optimization of the experimental conditions was performed to achieve the highest efficiency in substrate degradation, and fundamental insights into the mechanism of the MNP-BBS Fenton-like reaction were obtained.