SummaryContinuous monocropping degrades soil physicochemical properties, leads to the accumulation of toxic compounds and changes soil microbial community composition. Pre-flooding the soil is a promising strategy to improve its productivity; however, little is known about the underlying mechanisms. Here, strawberry (Fragaria × ananassa) pot experiments were conducted with soil that had been used for continuous monocropping. The treatments were pre-flooding alone, with rice straw added and with rice straw plus a biofertilizer (mainly contained Bacillus velezensis) amendment, and the impacts of the treatments on soil physicochemical properties, bacterial diversity and composition and the integrated plant-soil-microbe responses were tracked. The strawberry biomass significantly increased after pre-flooding treatments. Pre-flooding increased the soil pH and the available P and K concentrations, while it decreased soil electrical conductivity. The bacterial diversity and abundance significantly increased after pre-flooding treatments. A Mantel test showed that soil pH and salinity were the two most important factors in shaping bacterial composition, but they exerted opposite effects. The increased strawberry biomass after pre-flooding was significantly correlated with bacterial composition and soil salinity in long-term continuous strawberry monocropping systems.