Abstract Soil phosphorus (P) availability is a crucial factor determining primary productivity in terrestrial ecosystem. Plant functional traits and microbes under P‐deficient conditions can respond positively to increase soil P bioavailability. Whether and/or how the fine‐root traits (FRTs) of deep‐rooted desert species affect the rhizosphere and bulk soil community of phoD‐harbouring bacteria and thus improve the availability of soil P, however, remains unclear. We conducted a three‐year artificial outdoor pot experiment of P supply using Alhagi sparsifolia Shap. (hereafter Alhagi) to address this gap. Fine‐root samples from 1‐ and 3‐year‐old Alhagi seedlings and samples of the rhizospheres and bulk soil were collected. High‐throughput sequencing, sequential extraction and root system scanning were used to determine soil phoD‐harbouring bacteria community, Hedley‐P fractions and the FRTs. Fine‐root surface area (RSA), specific root length, foliar Mn concentration (indicating the quantities of root carboxylates that are released) and acid phosphatase (APase) activity were significantly higher in the no‐P supply compared with the high‐P supply conditions. APase activity was significantly higher by 27%, but the foliar Mn concentration was remarkably lower by 26%, in the 3‐ than the 1‐year‐old seedlings. The rhizospheric concentrations of labile P, moderately labile P, inorganic P and organic P in the no‐P supply condition were 5%, 11%, 10% and 21% higher, respectively, in the 3‐ than the 1‐year‐old seedlings. RSA and the foliar Mn concentration were dominated root predictors for the rhizospheric phoD‐harbouring bacteria community for the 1‐year‐old seedlings, whereas fine‐root P concentration was the dominated root predictor for the rhizospheric and bulk soil phoD‐harbouring bacteria communities for the 3‐year‐old seedlings. Soil water content, as the most dominant soil factor driving the variation of phoD‐harbouring bacteria community, notably could not be ignored. FRTs were the main factors that directly and positively determined rhizospheric phoD‐harbouring bacteria community and thus influenced soil P availability, but bulk soil phoD‐harbouring bacteria community were dominated by inorganic P concentration. The importance of fine‐root morphological traits to soil P availability gradually increased as the plants grew. Overall, our results emphasize the significance of rhizospheric phoD‐harbouring bacteria determined by the effect of FRTs on the bioavailability of soil P. Read the free Plain Language Summary for this article on the Journal blog.