With the objective of developing a post-treatment process for anaerobically digested livestock wastewater, an innovative natural treatment system composed of two units is proposed. The first trickling filter unit further reduced biochemical oxygen demand and achieved a certain degree of nitrification. The second soil-plant unit was targeted at the removal and recovery of nutrients N, P and K. For the feasibility study, a bench-scale soil column test was carried out, in which red ball earth and alfalfa were utilized for treating synthetic nutrient-enriched wastewater. Through long-term operation, the nitrification function was well established in the top layers, especially the top 20 cm, although a supplementary denitrification process was still required before discharge. P and K were retained by the soil through different mechanisms, and their plant-available forms that remained in the soil were considered suitable for indirect nutrient reuse. As for alfalfa, with wastewater application it fixed more N from the atmosphere, and directly recovered 6% of P and 4% of K input from wastewater. More importantly, alfalfa was verified to have an indispensable role in stimulating the soil nitrifying microorganisms by sustaining their abundance during substrate (NH3) and oxygen scarcity, and enhancing cell-specific nitrification potential during substrate (NH3) and oxygen sufficiency. The proposed system is expected to be further improved, and adopted as a sound countermeasure for livestock wastewater pollution.