Background and aims <p>Legume-based crop rotation is an effective practice for increasing soil phosphorus (P) availability and crop P uptake, with soil microorganisms playing a crucial role in this process. However, how long-term legume-based rotations affect the diversity of key P-mobilizing microbial guilds and their links to soil P cycling remains unclear.</p> Methods <p>This study examined soil P cycle multifunctionality and <i>phoD</i>- and <i>pqqC</i>-containing bacterial communities in thirty-eight‑year wheat-fallow and legume-based wheat rotation systems (a wheat-pasture and a wheat-crop rotation).</p> Results <p>Wheat-crop rotation enhanced soil P cycle multifunctionality and its associated variables, increasing available P by 6.8–17.8%, microbial biomass P by 48.3–71.4% and alkaline phosphatase activity by 11.2–29.9%. Wheat-pasture rotation also increased the capacity of soil iron phosphate mobilization. The community composition of <i>phoD</i>- and <i>pqqC</i>-containing bacteria varied among the cropping systems. For <i>phoD</i>-containing bacteria, soil nutrient ratios (mineral N:available P, microbial biomass C:N) and microbial biomass C were the main predictors, while for <i>pqqC</i>-containing bacteria, mineral N and available P were the key predictors. Wheat-crop rotation soil is characterized by a substantial number of indicator taxa for <i>phoD</i>-containing bacteria, which were notably different from those in wheat-pasture rotation soil. Conversely, fewer indicator taxa for <i>pqqC</i>-containing bacteria were identified across the cropping soils. Changes in community composition/alpha diversity of overall and indicator taxa of <i>phoD</i>- and <i>pqqC</i>-containing bacteria were important drivers of soil P cycle multifunctionality.</p> Conclusion <p>Our findings highlight that legume-based rotations significantly shape communities of <i>phoD</i>- and <i>pqqC</i>-containing bacteria in soil, potentially enhancing soil P cycle multifunctionality.</p>