A method and an apparatus for sterilizing packaging material for use in packaging for protein containing products, such as food products or medical drugs. The packaging material is sterilized by irradiating it using a beam of ionizing radiation, such as an electron beam or a beam of gamma rays. Afterwards, the packaging material is processed in such a manner that protein reactive substances or compounds formed in the packaging material during the irradiation step are at least partly removed or rendered inreactive with respect to proteins. The processing step may advantageously be performed by heating the packaging material. Preferably, the processing step involves accelerating diffusion from the packaging material of protein reactive substances or compounds. Since the protein reactive substances or compounds are removed or rendered inreactive with respect to proteins, degradation of the product which is later stored in the packaging material is considerably reduced. The packaging material needs to be stored under sterile conditions for a shorter period of time. Thereby the space needed for sterile storage, as well of the risk of contamination, is considerably reduced.