Cold atmospheric plasma (CAP) is a non-thermal technology that could be applied for food decontamination from both biological (microorganisms) and chemical (pesticides, food allergens, mycotoxins) contaminants, thanks to the production of reactive species (RS). However, RS could also promote the onset and the progress of food lipid oxidation, which may limit the quality and acceptability of the final products. The aim of this work was to assess the oxidation degree of pistachio kernels after treatment in a surface dielectric barrier discharge (SDBD). Two different operative conditions for CAP generation were investigated, resulting in the production of high (800 ppm) or low (300 ppm) concentrations of ozone. Limited amounts of hydroperoxides (3.00–4.22 mEq O2/kg), thiobarbituric acid reactive substances (TBARS, 0.072–0.600 mg TEP/g oil), and phytosterol oxidation products (POPs, 14.43–17.20 μg/g) were observed in lipids of both control and plasma processed pistachios. Plasma treatments did not significantly affect the total fatty acid composition and the amounts of identified unsaponifiable matter constituents (4-desmethylsterols, 4,4-dimethylsterols, 4-methylsterols), except for an unexpected significant increase of γ-tocopherol content in extracted oils. These findings contribute to gaining further knowledge for the scale-up of CAP technology to industrial processing.