Background and aims <p>Iron (Fe) and zinc (Zn) are critical micronutrients for plant growth, yet the molecular mechanisms governing their tissue-specific distribution and signaling in wheat are in their infancy, and there are still many specific issues that are not clear. The aim of this study is to investigates the transcriptional responses underlying Fe or Zn homeostasis—particularly in the shoot basal region and youngest leaf—under deficiency stress.</p> Methods <p>A comparative transcriptomic approach and phenotypic analysis were applied to roots, shoot basal regions, and youngest leaves of hexaploid wheat (<i>Triticum aestivum</i> cv. Fielder) following one-week exposure to Fe- or Zn-deficient hydroponic conditions. Differential gene expression was analyzed to pinpoint genes and transcription factors (TFs) associated with Fe or Zn distribution and signaling.</p> Results <p>Fe deficiency induced chlorosis in the youngest leaf, while Zn deficiency reduced Zn accumulation in the shoot basal region. Transcriptome profiling identified VIT/VTL, IMA, and ZIP genes as dual regulators of Fe and Zn distribution, whereas NAAT, DMAS, FRO, YSL, OPT, and ZIFL exhibited specificity to Fe distribution. TF families displayed specialized roles: MYB potentially coordinates both Fe and Zn homeostasis, while bHLH and NAC were linked to Fe distribution, and bZIP to Zn allocation. Signaling pathways further diverged, with bHLH, bZIP, and WRKY TFs predominantly associated with Fe signaling.</p> Conclusions <p>This study uncovers tissue-specific regulatory divergence in wheat under Fe or Zn deficiency, delineating shared and distinct molecular networks for micronutrient distribution and signaling.</p>