The present study was designed to study the effect of drought on root, stem and leaf anatomy of Astragalus gombiformis Pomel. Several root, stem and leaf anatomical parameters (cross section diameter, cortex, root cortical cells, pith, leaf lamina and mesophyll thickness) were reduced under moderate to severe water deficit (20–30 days of withheld irrigation). The stele/cross section root ratio increased under moderate water deficit. The root’s and stems vascular systems showed reduced xylem vessel diameter and increased wall thickness under water deficit. In addition, the root xylem vessel density was increased in these drought conditions while it was unchanged in the stems. The stomata density was increased under prolonged drought conditions whereas the stomata size was untouched. The leaf vascular system showed reduced xylem and phloem tissue thickness in the main vein under moderate to severe water deficit. However, in the lamina the vascular tissue and the distance between vascular bundle were unaffected. Our findings suggest a complex network of anatomical adaptations such as a reduced vessel size with increased wall thickness, lesser cortical and mesophyll parenchyma formation and increased stomata density. These proprieties are required for the maintenance of water potential and energy storage under water stress which can improve the resistance of A. gombiformis to survive in arid areas.