Iron (Fe) is an essential element for all organisms. Fe deficiency can limit plant production and cause anaemia in humans. The improvement of Fe homoeostasis could resolve both problems. Fe homoeostasis in Aegilops tauschii, the D genome donor of bread wheat, is not fully understood. Here, we analysed physiological traits in 42 accessions of Ae. tauschii associated with Fe homoeostasis, i.e. mugineic acid family phytosiderophores (MAs), phenylamides, SPAD values and metal concentrations. All traits showed diversity, suggesting the presence of candidate genes in the Ae. tauschii accessions, which could improve Fe homoeostasis in bread wheat. All accessions mainly produced and secreted mainly 2′-deoxymugineic acid among MAs, but eight of them secreted unknown products from their roots under Fe deficiency. It was revealed that 15 kinds of phenylamides and 2 kinds of bread wheat phytoalexins were produced in Fe-deficient roots of Ae. tauschii. Multivariate and principal component analyses showed that chlorophyll content was correlated with shoot Fe concentration. Genome-wide association study analysis associated several genomic markers with the variations in each trait analysed. Our results suggest that Ae. tauschii has alleles that could improve Fe homoeostasis to generate Fe-deficiency-tolerant or Fe-biofortified bread wheat.