Organic matter and nitrogen in livestock manure was pre-treated by gamma irradiation. The optimal dose ranged 30–50 kGy for solubilization of organic matter and nitrogen. Carbohydrates and proteins increased with the applied dose. Lipids did not show a regular increase pattern. A large amount of organic nitrogen in livestock manure was solubilized after gamma irradiation. The pre-treated livestock manure was treated using a bioelectrochemical ion-exchange reactor. High removal of organic matter and nitrogen was achieved with the applied dose of 50 kGy. The maximum 88.5% of chemical oxygen demand removal was obtained in the bioelectrochemical ion-exchange reactor due to readily biodegradable chemical oxygen demand fraction. Nitrogen removal was significantly affected by ammonia flux of ion-exchange membrane between anaerobic and aerobic chamber. With a high ammonia flux of 4.7513 mg/m2/sec, the maximum ammonia removal was 79.1%.