Methods and systems for the terminal sterilization and surface decontamination of prefilled containers containing sensitive drug products, such as biotech drug products that are otherwise temperature or radiation sensitive, and thus not suitable for terminal sterilization by classical methods involving steam or gamma rays. The methods and systems are especially suited for prefilled containers in secondary packaging. Methods include terminal sterilization by exposing prefilled containers in secondary packaging to tunable-beta radiation and further include terminal sterilization by exposing prefilled containers to controllable vaporized-hydrogen peroxide, including application of measures to reduce or prevent diffusion of vaporized-hydrogen peroxide into prefilled containers.