The effects of argon and nitrogen cold plasma treatments on the lipolytic enzymes activity in wheat germ were investigated. Using argon as plasma gas, the residual activity of lipase and lipoxygenase decreased to 42.50% and 87.72%, respectively after 30 min. Switching plasma input gas to nitrogen, the residual activities of lipase and lipoxygenase after the same time of atmospheric cold plasma (ACP) treatment were 77.50% and 92.52%, respectively. The antioxidant potential and phenolic compounds show no significant difference during ACP duration. However, the remaining activities of lipase and lipoxygenase after 30 min steam autoclaving were 6.25% and 18.60%, respectively. Also, the antioxidant activity and total phenolic content reduced by 14.70% and 30.80%, respectively. In brief, the ACP treatment efficiency was function of the input gas and the treatment time. The presented results about the input gas impacts would be useful in industrial development of ACP application for wheat germ stabilization.