Re-using and adding value to by-products is one of the current focuses of the agri-food industry, following the Sustainable Development Goals of United Nations. In this work, the by-products of four plants, namely chestnut burr, acorn peel, olive leaf, and grape stem were used as coagulants to treat elderberry wastewater (EW), a problematic liquid effluent. EW pre-treatment using these natural coagulants showed promising results after pH and coagulant dosage optimization. However, the decrease in total organic carbon (TOC) was not significant, due to the addition of the plant-based natural coagulants which contain carbon content. After this pre-treatment, the photo-Fenton advanced oxidation process was selected, after preliminary assays, to improve the global performance of the EW treatment. Photo-Fenton was also optimized for the parameters of pH, H2O2, Fe2+, and irradiance power, and the best conditions were applied to the EW treatment. Under the best operational conditions defined in the parametric study, the combined results of coagulation–flocculation–decantation (CFD) and photo-Fenton for chestnut burr, acorn peel, olive leaf, and grape stem were, respectively, 90.2, 89.5, 91.5, and 88.7% for TOC removal; 88.7, 82.0, 90.2 and 93.1%, respectively, for turbidity removal; and finally, 40.6, 42.2, 45.3, and 39.1%, respectively, for TSS removal. As a final remark, it is possible to suggest that plant-based coagulants, combined with photo-Fenton, can be a promising strategy for EW treatment that simultaneously enables valorization by adding value back to food by-products.