Soil phosphorus (P) availability is a crucial factor determining primary productivity in terrestrial ecosystems. 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-harboring 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 one- and three-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-harboring 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 to the high-P supply conditions. APase activity was significantly higher by 27%, but the foliar Mn concentration was remarkably lower by 26%, in the three than the one-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 three- than the one-year-old seedlings. RSA and the foliar Mn concentration were dominant root predictors for the rhizospheric phoD-harboring bacteria community for the one-year-old seedlings, whereas fine-root P concentration was the dominant root predictor for the rhizospheric and bulk-soil phoD-harboring bacteria communities for the three-year-old seedlings. Soil-water content, as the most dominant soil factor driving the variation of phoD-harboring bacteria community, notably could not be ignored. FRTs were the main factors that directly and positively determined the rhizospheric phoD-harboring bacteria community and thus influenced soil P availability, but bulk-soil phoD-harboring 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-harboring bacteria determined by the effect of FRTs on the bioavailability of soil P.