The thermal processing of almond kernels implies the use of techniques that produce chemical changes such as oxidation. Phytoprostanes (PhytoPs) are considered biomarkers of the oxidative stress in plants. We studied the PhytoP profile in kernels of almond cultivars under different conditions, in relation to packaging, temperature and time of storage and processing. The most abundant PhytoP was the F1t series. The PhytoP levels increased significantly with the time of storage (3 and 6months) and the total PhytoP concentration was higher under air than in a vacuum packaging atmosphere. Storage at 24°C raised the concentrations of individual PhytoPs and the total sum of PhytoPs. The frying and roasting processes led to a strong reduction of the original concentration of most PhytoPs and promoted the synthesis of specific PhytoPs that were not detected in raw kernels and thus could be biomarkers of the degree of oxidative degradation of almonds.