Climate change is expected to alter the frequency and intensity of drying and rewetting cycles, impacting water availability and consequently soil nutrient availability. However, the effects of these fluctuations on the chemical speciation and bioavailability of phosphorus (P) in soil with or without desert species remain uncertain. We conducted a pot experiment involving bare soil and two desert species (Alhagi sparsifolia and Calligonum mongolicum) to determine the short-term impacts of drought (no water supply), drying-rewetting-1 (D-RW1, high frequency of low water amounts), and drying-rewetting-2 (D-RW2, low frequency of high-water amounts) treatments on soil Hedley-P pools, plant P concentration and biomass accumulation. Results demonstrated that the presence of plants significantly increased soil labile-P and organic P (Po) concentrations by 60–150% and 1–68%, respectively, compared to bare soil. Both D-RW1 and D-RW2 treatments significantly increased soil dissolved organic carbon concentration by 2–35% relative to the drought treatment. Moreover, soil resin-P and NaHCO3-Pi concentrations under Alhagi sparsifolia in D-RW1 treatment significantly increased by 31% and 75%, respectively, when compared to the drought treatment, with NaHCO3-Po and NaOH-Po concentrations under D-RW2 treatment rising by 14% and 32%, respectively. Furthermore, D-RW2 treatment significantly increased leaf P concentration and biomass compared to D-RW1 and drought treatments. Overall, compared to drought treatment, frequent low-intensity drying-rewetting cycles enhanced soil Pi turnover, whereas infrequent high-intensity drying-rewetting cycles increased Po turnover and P bioavailability. These findings will inform better water management strategies for desertification restoration in hyper-arid desert ecosystems.