In this study, our aim is to compare the inactivation of bacteria by direct plasma exposure of bacterial solution and plasma activated water (PAW) using a surface micro-discharge (SMD). Four potential factors which could affect both treatments were tested, namely the effect of low dose reactive oxygen species (ROS) pretreatment, enzymatic defence mechanism against oxidative stress, extracellular molecules, and mass transfer in liquid. We applied two power modes of the SMD, i.e. low power ozone mode and high power mode, to inactivate () in distilled water either by direct treatment (DT) or PAW. ROS pretreatment was tested by 30 M of , while superoxide dismutase (SOD) and catalase were used to investigate the effect of enzymatic antioxidant defense. Furthermore, the effect of extracellular molecules was examined by centrifuging and mass transfer in liquid by vortexing. In addition, reactive species in the solution were measured by titanium sulfonate, and nitrite/nitrate colorimetric method for , and and , respectively. Results indicate that vortexing and centrifuging significantly influence the bacterial reduction, while pretreatment could not induce resistance of bacteria against plasma treatment. Enzymatic antioxidants of SOD and catalase could potentially effect the inactivation and plasma chemistry yet only if the concentrations are sufficiently high. We assume that the continuous generation of peroxynitrite is crucial in plasma inactivation for both DT and PAW under high power condition, while under low power condition, long-term bactericidal affects are limited due to the decomposition of ozone by nitrite.