Soil phosphorus (P) availability is a critical factor influencing plant productivity and the capacity of terrestrial ecosystems to sequester atmospheric carbon. However, the effects of long-term anthropogenic disturbance on Pcycling processes in hyperarid desert ecosystems remain insufficiently characterized. A 16-year experiment was conducted to examine the effects of no-disturbance (CK), spring harvest, autumn harvest, fire, and irrigation treatments on P dynamics in desert deep-rooted plants, soil, and microbial biomass across soil layers (0-150 cm). Additionally, the types and abundances of genes and signature microbes involved in microbial P-cycling processes (MPCPs) were analyzed in the topsoil (0-15 cm) and subsoil (100-150 cm). The findings indicate that aboveground biomass per plant increased by an average of 3.6-fold in the harvest and fire treatments compared to CK. However, aboveground plant P concentrations and soil bioavailable P decreased by 17.9% and 14%, respectively, across all disturbance treatments. Soil organic carbon (SOC) declined by 13%, primarily in the topsoil, whereas the subsoil exhibited enhanced potential for inorganic P (Pi) solubilization and organic P (Po) mineralization. The regulation of soil bioavailable P and active Po in the topsoil was primarily associated with SOC, whereas subsoil P dynamics were influenced by key MPCPs-related genes and signature microbes. This study provides insights into the trajectory of plant-soil-microbial P interactions under long-term anthropogenic disturbance in hyperarid desert ecosystems and highlights the potential risk of P depletion in desert soils. Mitigating anthropogenic disturbances is identified as a critical strategy for the management and restoration of these ecosystems.