Aim: This study investigated the effect of Atmospheric cold plasma (ACP) exposure induced stress on microbial inactivation patterns and the regulation of genes involved in the microbial stress response in conjunction with key processing parameters of exposure time and post treatment storage time. Methods and Results: Cell suspensions of Escherichia coli BW 25113 and its isogenic knock-out mutants in rpoS, soxR, soxS, oxyR and dnaK genes were treated with high voltage ACP in a sealed package for 1, 3 and 5 min followed by 0, 1 and 24 h post-treatment storage. ROS densities and colony formation were determined. ΔrpoS strain showed higher microbial reduction and greater cell permeability than other mutants, while ΔoxyR only showed this effect after 5 min treatment. With increased post-treatment storage time, ΔsoxS and ΔsoxR had increased sensitivity and resistance, respectively. ΔdnaK cell suspensions had much higher ROS than other strains and showed increased sensitivity with 24 h post-treatment storage. Conclusions: RpoS and oxyR genes have both short-term and long-term regulatory effects under plasma stress. However, knocking out dnaK gene had an immediate response on ROS scavenging and long-term repairing mechanisms. ΔsoxR and ΔsoxS had different responses to ACP treatment with the increase of post-treatment time in relation to clearance of reactive species implying the different characteristics and functions as subunits. Significance and Impact of study: By comparing the response of mutants under ACP exposure to key processing parameters, the mechanism of microbial inactivation was partly revealed with respect to cellular regulation and repairing genes.