The effect of long-term storage on the carotenoid composition in durum wheat and tritordeum grains was studied. Total carotenoid (mainly lutein) content decreased according to a temperature dependent first-order degradative kinetic model. The carotenoid retention was similar in both genotypes at the lower temperatures (71–73% at −32°C, 70% at 6°C and 55–56% at 20°C), whereas at the higher temperatures the pigment retention was higher in tritordeum (42% at 37°C; 10% at 50°C) than durum wheat (23% at 37°C; 1% at 50°C), probably due to the greater proportion of esterified xanthophylls. A clear difference between free and esterified pigments was observed, with smaller losses and slower degradation (higher stability) observed for the latter. The xanthophyll esterification process was highly specific and had a significant effect on the carotenoid stability according to the fatty acids involved in the esterification and their position on the lutein molecule. The results were consistent with a degradation process in which the carotenoid behavior is influenced by the chemical structure. Xanthophyll esterification can be promoted by environmental conditions, regardless of the cereal genotype, and is a powerful tool to modulate the carotenoid profile in cereals.