The exploitation of organic waste as a source of bio-based substances to be used in environmental applications is gaining increasing interest. In the present research, compost-derived bio-based substances (BBS-Cs) were used to prepare hybrid magnetic nanoparticles (HMNPs) to be tested as an auxiliary in advanced oxidation processes. Hybrid magnetic nanoparticles can be indeed recovered at the end of the treatment and re-used in further water purification cycles. The research aimed to give new insights on the photodegradation of caffeine, chosen as marker of anthropogenic pollution in natural waters, and representative of the contaminants of emerging concern (CECs). Hybrid magnetic nanoparticles were synthetized starting from Fe(II) and Fe(III) salts and BBS-C aqueous solution, in alkali medium, via co-precipitation. Hybrid magnetic nanoparticles were characterized via X-ray diffraction (XRD), thermo-gravimetric analysis (TGA) and Fourier transform infrared (FTIR) spectroscopy. The effect of pH, added hydrogen peroxide, and dissolved oxygen on caffeine photodegradation in the presence of HMNPs was assessed. The results allow for the hypothesis that caffeine abatement can be obtained in the presence of HMNPs and hydrogen peroxide through a heterogeneous photo-Fenton mechanism. The role of hydroxyl radicals in the process was assessed examining the effect of a selective hydroxyl radical scavenger on the caffeine degradation kinetic.