The inactivation of bacteria by plasma discharges offers the unique benefits of short treatment times, minimal damage to the objects being sterilized and minimal use of hazardous chemicals. Plasmas produce reactive fluxes of ions, atoms and UV photons from any given precursor gas and are expected to be a viable method for such sterilization applications. The plasma based inactivation of harmful biological systems is, however, not yet widely used, because any validation is hampered by the limited knowledge about the interaction mechanisms at the interface between a plasma and a biological system. By using quantified beams of hydrogen atoms, argon ions and UV photons, the treatment of bacteria in a typical argon–hydrogen plasma is mimicked in a very controlled manner. As an example the inactivation of endospores of Bacillus atrophaeus is studied. It is shown that the impact of H atoms alone causes no inactivation of bacteria. Instead, the simultaneous impact of atoms and low energy ions causes a perforation of the endosporic shell. The same process occurs during plasma treatment and explains the efficient inactivation of bacteria.