Emerging plasma technology has demonstrated its effectiveness in inactivating bacteria and spores, showing wide applicability in environment cleaning and in the food supply chain. Studies have revealed that the main reason of plasma-mediated bacterial inactivation were contributed to the oxidative damage on inner membranes (IMs) of cell, while few research paid attention to the oxidation stress process of lipid in spores’ IMs. This study investigated the impact of atmospheric pressure plasma jet (APPJ) treatment on spore inactivation, focusing on oxidative stress mechanisms and changes in membrane lipid composition. Results demonstrated that APPJ treatment induced significant oxidative stress within spores, characterized by elevated levels of reactive oxygen and nitrogen species (RONS). This oxidative stress led to the peroxidation of glycerophospholipids, particularly phosphatidylglycerol, phosphatidylcholine, and cardiolipin, major components of spore membranes. Subsequently, the rearrangement of membrane lipid and the formation of lipid hydroperoxide, caused by the released cations and RONS, accelerated membrane instability. These changes correlated with increased membrane permeability and structural damage observed via flow cytometry, indicating the critical role of membrane lipid peroxidation in spore inactivation. Furthermore, the study highlighted the potential of APPJ as a robust technology for enhancing food safety by targeting spore-forming pathogens throughout the food supply chain.