This study investigates the effect of storage temperature on carotenoid composition in durum wheat and tritordeum whole-grain flours. For both cereal genotypes, total carotenoid content significantly decreased during storage, following a temperature dependent first-order kinetic model. Individual and total carotenoid content decay were similar for durum wheat, with a maximum at 50 °C at the end of the storage period (94%). In contrast, the evolution of lutein ester fractions in tritordeum showed lower losses than for free lutein (∼ 50%), and consequently the total carotenoid content was less affected (83%). A decrease in the lutein monoesters fraction was observed, coinciding with an increase in the diesterified forms, especially for lutein dilinoleate. These data suggest an esterifying activity in flours different from the enzyme systems operating in vivo (xanthophyll acyl transferase). The formation of lutein diesters, with greater stability, explains the slower carotenoid degradation in tritordeum whole-grain flours.