Background and aimsSoil microbial phosphorus (P) cycling plays a pivotal role in ecosystem nutrient dynamics, yet its response to vegetation restoration under varying water availability, especially in alpine areas remains poorly characterized.MethodsWe integrated metagenomic sequencing with a revegetation chronosequence to systematically evaluate how restoration duration and water availability shape microbial P-cycling processes in degraded meadow and desertified steppe soils.ResultsRestoration significantly increased moderately labile, stable, and total P fractions in degraded meadow soils, whereas its impact on desertified steppe soils was negligible. Notably, water availability emerged as a critical driver of both microbial community composition and the abundance of P-cycling genes. For instance, Proteobacteria dominated microbial communities in degraded meadow soils, while Proteobacteria and Acidobacteria coexisted as keystone taxa in desertified steppe soils. Furthermore, key P-cycling genes (e.g., gcd and phoD) exhibited contrasting patterns across ecosystems. The gcd gene, associated with inorganic P solubilization, was more abundant in water-limited desertified steppe soils. Structural equation modeling further clarified that in desertified steppe soils, water availability primarily regulated P transportation pathways, whereas in meadow soils, it directly influenced genes governing inorganic P solubilization and organic P mineralization.ConclusionsThese findings underscore the intricate interplay between water regimes, microbial community structure, and P-cycling functionality during restoration. Our study highlights the necessity of tailoring restoration strategies to water conditions and temporal dynamics to optimize microbial-mediated P cycling.