Riparian zones in deserts are critical for water purification, habitat, and soil conservation, but most studies focus on vegetation zones without long-term monitoring, hindering the comprehensive assessment of their long-term benefits. This study on Yuangeda Lake in northwestern China's desert used spatiotemporal substitution to convert soil spatial heterogeneity into a temporal gradient, analyzing soil properties across vegetation zones formed by lake expansion and microbial impacts on amino acid nitrogen. Results showed that rhizosphere soil amino acid nitrogen was higher in grass (Agropyron cristatum L. Gaertn.) and grass/shrub mixed (A. cristatum and Artemisia desertorum Spreng.) areas than in shrub areas (A. desertorum). As plant communities persisted, a distinct threshold in rhizosphere soil amino acid nitrogen emerged at approximately 11 years. Rhizosphere bacterial and fungal specific taxonomic units, microbial co-occurrence network topologies, and amino acid nitrogen-related bacterial functions differed between grass/grass-shrub-mixed and shrub areas, linked to plant community duration. Bacteria dominated amino acid nitrogen formation in grass areas, while bacteria and fungi contributed in the grass/shrub mixed area. Overall, water inflow promoted soil amino acid nitrogen accumulation, with microbial contributions varying by plant community duration. This study supports desert riparian soil restoration and management, advancing our understanding of amino acid nitrogen in the nitrogen cycle.