Aims: Characterize the response of Deinococcus radiodurans R1 cells to low-pressure low-temperature nitrogen-oxygen microwave plasma and identify repair processes during recovery. Methods and Results: Cells coated onto glass slides exhibited a biphasic plasma inactivation kinetics. Treatment with various plasmas and subsequent incubation in recovery medium prolonged the lag phase in a part of the survivors, during which the ability to grow on stress medium was recovered. This recovery strongly depended on transcriptional and translational processes and cell wall synthesis, as revealed by addition of specific inhibitors to the recovery medium. Genes involved in DNA repair, oxidative stress response, and cell wall synthesis were induced during recovery, as determined by quantitative RT-PCR. Damage to chromosomal DNA caused by plasma agents and repair during recovery was directly shown by quantitative PCR. Plasmas with less UV radiation emission were also effective in killing D. radiodurans cells but resulted in less DNA damage and lower induction of the investigated genes. Conclusions: The response of D. radiodurans to plasma indicates that DNA, proteins, and cell wall are primary targets of plasma finally leading to the cell death. Protein oxidation is more important for killing of D. radiodurans cells than of Bacillus subtilis spores. Thus, the contaminating biological material affects the plasma composition to be used for sterilization. Significance and Impact of the Study: The results in this study provide new insight into the interaction of plasma with bacterial cells. This knowledge contributes to the definition of useful parameters for novel plasma sterilization equipment to control process safety.