The generation of waste in agricultural and livestock industries, followed by inadequate treatment and uncontrolled disposal to natural recipients, results in significant environmental pollution. Thus, the efficient and integrated management of high-organic-load waste produced in such activities is a key factor for sustainability and the protection of aqueous matrices. In this work, we investigate an integrated management approach for the treatment of agricultural, high-organic-load waste via a combination of processes, with an ultimate goal to improve the characteristics of the final waste and enhance the valorization of the nutrients contained in it. Towards this direction, a waste mixture comprising pig waste, cheese dairy, and food residues was sequentially treated in a laboratory scale by anaerobic digestion, followed by activated sludge (aerobic–anoxic treatment), and last by adsorption using natural zeolite. The efficiency of two different adsorption routes was examined (magnetically agitated zeolite or packed zeolite column), while the effect of the granule sizes of zeolite (0–1 mm or 1.5–3 mm) was also evaluated with regards to the remediation of the final effluent. Excellent adsorption capacities were observed in all cases, with the larger-sized zeolite exhibiting a superior performance, while the granule size of zeolite significantly affected the lifetime of the packed columns, as the smaller-sized zeolite columns reached their saturation point faster than the larger-sized zeolite analogue. The average ammonium nitrogen removal in the column experiment was ~92%, while total phosphorus was ~68%, respectively. Overall, an almost complete remediation of the final effluent was observed when compared with the physicochemical parameters of the initial waste, with a ~96% chemical oxygen demand, ~79% total nitrogen, ~96% total phosphorus, and ~82% phenols concentration decrease, signifying the high performance of the sequential treatment strategy proposed herein.