In this investigation, a new, green photo-Fenton process for wastewater treatment is proposed, involving the use of a natural iron source and natural additives, deriving from wastes, acting as iron chelators. The use of mineral iron as precursor in the photo-Fenton process, instead of iron salts, was still able to promote E. coli inactivation. Furthermore, the addition of four low weight organic acids (citric, tartaric, ascorbic and caffeic) showed a significant enhancement of the process, reaching total inactivation except for caffeic acid, which showed no significant effects. Two natural products, rich in the promising organic acids were tested as additives, lime and orange juice, plus their infusion. Lime-based additives showed better results compared to orange-based ones, which could be attributed to the excessive addition of organic matter in the orange systems. The formation of photoactive complexes with the mineral iron and the organic acids from the natural products induced the production of reactive species and ferrous ion, sustaining a homogeneous Fenton reaction. Finally, the proposed modified process was tested against different secondary effluents from a municipal wastewater treatment plant. Total bacterial inactivation was reached in the lime-based system, with no visible microorganism regrowth after 48 h. Additionally, the process was able to eliminate 40% of the total identified micropollutants of the secondary effluent reaching almost 50% of removal of the total effluent organic matter.