This study evaluates and compares sustainable, low-cost biofilter media, specifically chitosan and Phragmites australis biochar, with commercial activated carbon to remove chemical oxygen demand (COD) and phenol from agro-food industry wastewater. The primary objective is to identify an effective and eco-friendly alternative to conventional adsorbents for the post-treatment of effluents from Upflow Anaerobic Sludge Blanket (UASB) reactors. COD and phenol are targeted due to their environmental significance; COD reflects overall organic pollution, while phenol is a toxic, persistent compound in oily industrial wastewater. Multi-level factorial design experiments optimized using three types of adsorbent materials with different doses to improve the Biofilter performance. COD removal and phenol were studied as a function of four experimental parameters: adsorbent materials, dose, contact time, and wastewater type. To minimize the number of experi ments, MINITAB Version 19 software conducted the experiments using a multi-level full factorial design, reducing the total number of experimental runs required while still capturing the interactions and effects of the different factors involved. The characterization investigation was carried out using X-ray diffractometry (XRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and Brunauer–Emmett–Teller (BET). The optimal conditions achieved a composite desirability of 0.9872, indicating a near-ideal balance for both responses. For COD removal, the maximum rate of 98.3721% was achieved under the optimal conditions with Phragmites australis biochar (Adsorbent Material 2), UASB effluent (Wastewater Type 2), a contact time of 90 min, and a dose of 6.5 g/L, yielding a desirability value of 0.97463. The maximum rate of 86.6766% for phenol removal was also attained under the same optimal conditions, yielding a desirability value of 1.0000, representing perfect optimization for phenol removal. A Life Cycle Assessment (LCA) was conducted to evaluate the environmental impacts associated with the treatment of UASB effluent and Arma wastewater using the three different adsorbent materials. The Phragmites australis biochar offers the most environmentally sustainable option for wastewater treatment. It significantly reduces greenhouse gas emissions, resource depletion, toxicity impacts, and energy use compared to Activated Carbon and Chitosan. This research is consistent with the United Nations Sustainable Development Goals (SDGs), namely SDG 6 (Clean Water and Sanitation) and SDG 12 (Responsible Consumption and Production). Our f indings have far-reaching implications for large-scale wastewater treatment, offering a greener and more sustainable future.