This study investigated the use of a hydroxyl-radicals-generated microbubble/catalyst (MB/Cat) system for removing organic pollutants, nitrogen, and phosphorous from liquid fertilizer produced by livestock wastewater treatment. Use of the MB/Cat system aims to improve the quality of liquid fertilizer by removing pollutants originally found in the wastewater. In addition, a reduction effect has been reported for antibiotics classified as representative non-biodegradable matter. Samples of liquid fertilizer produced by an aerobic biological reactor for swine wastewater treatment were first analyzed for initial concentrations of pollutants and antibiotics. When the MB/Cat system was applied to the liquid fertilizer, TCOD, TOC, BOD5, and NH3-N, and PO4-P removal efficiencies were found to be approximately 52%, 51%, 30%, 21%, and 66%, respectively. Additionally, Amoxicillin hydrate was removed by 10%, and Chlortetracycline HCl and Florfenicol were not present at detectable levels These findings confirm that the MB/Cat system can be used with livestock wastewater treatment to improve liquid fertilizer quality and to process wastewater that is safe for agricultural re-use.