Kernel oxidation susceptibility and pellicle darkening are among the biggest concerns regarding walnut quality. Monitoring oxidation is crucial to preserve quality from production to consumption. Chemical oxidation parameters (peroxide value and UV absorbances), fatty acid profile, tocopherols, phenols, and volatiles in ‘Chandler’ and ‘Howard’ kernels were studied at different time points during 28 weeks of storage to evaluate potential oxidation markers. During storage, peroxide value, UV absorbances, and volatiles concentration increased; oxidative stability, phenols, and tocopherols decreased, while fatty acid profile was unaffected. ‘Chandler’ had a lower peroxide value, K232, and K268; and higher kernel and oil oxidative stability compared to ‘Howard’. Phenols and tocopherols decreased 1.2-fold in ‘Chandler’ and 1.3-fold in ‘Howard’. Using multivariate analysis, samples were discriminated in three groups according with their oxidative levels. Increases of volatiles in oil and kernel were associated with higher oxidative levels. Pentanal, 2-methylpropanal, hexanal, (E)-2-pentenal, 3-octanone, octanal, (Z)-2-penten-1-ol, hexanol, (E)-2-octenal, 1-octen-3-ol, benzaldehyde, (E,E)-2,4-nonadienal, and hexanoic acid in kernels were adequate at distinguishing oxidation levels and as oxidative markers in walnuts. Kernel volatiles is a useful measurement for walnut oxidation during storage without any prior fat extraction.