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Direct interactions of plasma matter with living cells and tissues can dramatically affect their functionality, initiating many important effects from cancer elimination to bacteria deactivation. However, the physical mechanisms and biochemical pathways underlying the effects of non-thermal plasma on bacteria and cell fate have still not been fully explored. Here, we report on the molecular mechanisms of non-thermal plasma-induced bacteria inactivation in both Gram-positive and Gram-negative strains. We demonstrate that depending on the exposure time plasma induces either direct physical destruction of bacteria or triggers programmed cell death (PCD) that exhibits characteristic features of apoptosis. The interplay between physical disruption and PCD is on the one hand driven by physical plasma parameters, and on the other hand by biological and physical properties of bacteria. The explored possibilities of the tuneable bacteria deactivation provide a basis for the development of advanced plasma-based therapies. To a great extent, our study opens new possibilities for controlled non-thermal plasma interactions with living systems.