Plasma-based technologies, including plasma-activated water (PAW), offer the capability to deactivate microorganisms on fruits and vegetables, preserving their sensory and nutritional quality. Although many studies have reported a synergistic microbicidal effect between PAW and mild heating, the underlying chemical processes driving these effects remain unexplored. Our study aims to evaluate the microbicidal capacity of two PAW types, one containing NO2− (PAW-N) and the other H2O2 (PAW-H), as well as their mixture (PAW-M), at different temperatures, and to elucidate the underlying temperature-dependent chemical processes. Using E. coli DH5α as the target microorganism, we measured colony-forming units under varying exposure times for each PAW type and their mixture at 8 and 28 °C. Additionally, we determined the time-dependent concentrations of NO2−, H2O2, and NO3− in the mixture, and calculated the reaction rate constant for peroxynitrous acid generation. The kinetic study revealed a fivefold increase in the reaction constant between H2O2 and NO2− in PAW-M at 28 °C compared to 8 °C, leading to a significant rise in hydroxyl radical production. The microbicidal efficacy of PAW-M exceeded that of individual PAWs or temperatures. Moreover, this effect was significantly enhanced by mild heating, resulting in log reductions of 0.24, 0.34, 2.3 (at 8 °C) and 0.74, 2.3, 3.6 (at 28 °C) for PAW-H, PAW-N, and PAW-M, respectively, after a 10-min exposure. In conclusion, the synergistic effect between PAW and mild heating may be attributed to the accelerated reaction rate of peroxynitrous acid formation in an acidic medium, leading to heightened hydroxyl radical generation.