This study focused on both the degradation behavior of a β-lactam antibiotic, cephalosporin C (CEP-C) and abatement of antibiotic resistance genes from fermentation residues by gamma irradiation. The results were compared to those obtained by pyrolysis at both 130 °C and 165 °C. Both techniques were effective to remove CEP-C from the fermentation residues and the degradation rate of CEP-C was initially rapid and then slowed down. The removal efficiency of CEP-C reached 92% at 50 kGy and increased slightly to 96% at 100 kGy of gamma irradiation, which was comparable to 91% and 94% by pyrolysis at 130 °C for 5 min and 10 min, respectively.Raising the pyrolysis temperature to 165 °C increased the degradation rate of CEP-C, but could not increase its degradation extent. The competition of the other substances (like protein) having high content in the fermentation residues with the target CEP-C for reactive radicals formed in water radiolysis might be the major reason to limit the decomposition of CEP-C totally. The relative abundance of cephalosporin resistance gene, tolC was abated around 50% after gamma irradiation of 50 kGy and 76.4% after pyrolysis of 130 °C for 15 min. The content of soluble protein and polysaccharides increased remarkably after gamma irradiation and pyrolysis. Ionizing irradiation appears to be an attractive alternative to dispose antibiotics fermentation residues safely.