Thermophilic aeration and electrochemical reactions are well-established methods for wastewater treatment to reduce metallic content, organic and inorganic matter, turbidity, coloration, and nutrient levels. In this study, thermophilic aerobic oxidation (TAO) and electrocoagulation (EC) were implemented together to improve the quality of liquid fertilizer by reducing the nutrient load and toxicity of swine manure. The influent in this study was prepared by mixing anaerobic digestate and liquid swine manure at a 1:9 ratio and treating it for 3 days at 50–60 °C in a field-scale TAO system. The TAO effluent was then processed in an EC reactor for 180 min with a 30 V electric supply through two sets of iron and aluminum hybrid electrodes. The combined TAO and EC processes led to a germination index of 133% using the final efflux. The high retention of important nutrients such as total nitrogen and potassium, combined with the 100% reduction in heavy metals, over 60% reduction in trace minerals, and 89% reduction in pollutants in the final product, helped to achieve a higher germination index. Overall, the combination of TAO and EC was demonstrated to be an effective technique for enhancing the quality of liquid fertilizer derived from swine manure.