Drought is the main abiotic stress threatening wheat production in the Mediterranean region. While the negative effect of drought on the photosynthetic carbon and nitrogen metabolism of the flag leaf has been widely studied, little is known about its effect on other photosynthetic organs such as the ear. Our study compared the responses to water stress of organ temperature, spectral vegetation indices, nitrogen content, carbon isotope composition (δ13C) and expression of key genes for primary metabolism and drought-stress response in the flag leaf and the ear. Measurements were performed at heading and early grain filling in field-grown durum wheat under irrigated and rainfed conditions. Multivariate analysis of physiological traits and gene expression indicated that ears had a similar behaviour regardless of the water regime, while water stress led to significant negative effects on flag leaves. This better performance of ears under water stress compared to leaves was due to good nitrogen and water status and higher expression of key genes for primary metabolism and drought-stress responses, which also indicate a pattern of delayed senescence in ears. Upregulation of genes involved in respiration, CO2 refixation and nitrogen assimilation in ears may also suggest the relevance of these processes in ear metabolism under water stress. This study highlights the importance of including ear traits when unravelling the mechanisms that facilitate adaption of wheat to future environmental scenarios.