This invention relates to the pharmaceutical sector, specifically to an improved device for electron-beam irradiation sterilisation of flexible bags, in particular the type of flexible bags that may contain human plasma protein solutions for therapeutic use. This device comprises two electron accelerators: a first accelerator emitting an electron beam with energies between 400 and 500 keV and a second accelerator emitting an electron beam with an energy of at least 4 MeV. In addition, the present invention relates to a sterilisation method by electron-beam irradiation of such flexible bags and to an in-line filling process for flexible bags using the sterilisation device and method of this invention.