Seven composites of iron oxide nanoparticles embedded in organic microparticles mediated by Cu(II) were synthesized using yerba mate (Ilex paraguariensis) dry leaf extract as precipitant, capping agent, and dispersant medium, using different Cu/Fe molar ratios. A thorough characterization of the particles by transmission electron microscopy (TEM), X-ray diffraction (XRD), thermogravimetric analysis-mass spectrometry (TGA-MS), Fourier transform infrared spectrometer (FTIR), and atomic absorption-spectrometry (AA) indicates that all materials have spheric-like morphology with nanoparticles composed by metal oxide phases embedded into organic microparticles. Interestingly, this organic matter is proposed to play an important role in the solids' photocatalytic activity in a photo-Fenton reaction, in which iron photo-leaching was elucidated, and a mechanism through ligand-to-metal charge transfer processes was proposed. All materials showed catalytic activity in the methyl orange elimination, achieving discolorations up to 96% in 2h under UV irradiation at 375nm. An experimental correlation between all samples' UV/Vis spectra and their performances for methyl orange discoloration was observed. This process opens a landscape very interesting for the use of agroindustrial residues for green synthesis of metal oxide nanomaterials and their use and understanding of organo-metallic systems participation in Fenton-based processes.