Abstract Dioecious species may be particularly vulnerable to climate change because they often exhibit skewed sex ratios that are reinforced by the physiological and biological specialization of each sex to specific microhabitats. Yet, it is unclear how differences in functional traits between female and male plants lead to sex‐specific responses to drought and whether these responses are associated with phosphorus (P) acquisition diverge or converge. Here, we measured the morphological and physiological traits of roots, and the functional micro‐organisms related to P acquisition in Populus euphratica females and males in the rhizosphere under different water availability. The specific root length of females was greater than that of males, regardless of soil water availability. Therefore, the P concentration of females was significantly higher than that of males under well‐watered conditions. In contrast, the physiological adjustment to drought showed distinct sexual patterns: males significantly increased the foliar manganese concentration and maintained higher acid phosphatase activities in the rhizosphere. Moreover, the arbuscular mycorrhizal hyphal biomass reduced less in males than in females under water deficiency. Soil water shortage also decreased the α diversity of phosphate solubilizing bacteria (PSB) and changed the co‐occurrence network in the rhizosphere of females, but it had little effect on males. Consequently, the favourable physiological processes and effective maintenance of functional microbial homoeostasis in the rhizosphere were the reasons that enabled males to reduce P loss in leaves under water deficiency. Our study indicated that, within P. euphratica populations, covariations and trade‐offs simultaneously occurred among the three groups (root morphology, physiology and functional micro‐organisms) of functional traits evaluated. More generally, the assessment of variations in sex‐specific P acquisition strategies may help to understand the causes of sex ratio bias and how P. euphratica males and females mitigate resource shortage. Read the free Plain Language Summary for this article on the Journal blog.