A system and methods for sterilizing or disinfecting articles, particularly the hollow internal areas of medical instruments are disclosed. The system includes a plasma generator having an electrode, a shield, and a dielectric gap between the electrode and the shield. A source of electrical power is connected to the plasma generator for applying an electron energy density between the electrode and the shield. A source of gas comprising water vapor, oxygen and nitrogen provides a flow of gas between the electrode and the shield, to form a plasma containing acidic and/or oxidizing species. In the exemplary system, the temperature at the shield's surface is 0.05 eV/molecule of the gas. Also disclosed is a method for disinfecting an article contaminated with a bio-film or spores, by exposing the contaminated article to the plasma for an exposure time sufficient to achieve at least 2-log10 reduction in colony forming units.