AbstractLong‐term continuous cropping of strawberry induces soil degradation, which reduces strawberry growth and yield. Agricultural waste and microorganisms have great potential in improving soil health. The aim of this study was to identify the potential mechanisms of Bacillus velezensis containing agricultural waste to improve soil health. Soil that had been cropped continuously for more than 10 years was flooded with water for approximately 28 days. After flooding, agricultural waste fermented with microorganisms was applied to improve soil health. Microbial biofilm formation and rhizosphere colonization were also determined. Different agricultural waste coupled with pre‐flooding resulted in a significant increase of strawberry biomass by 33.0%–98.4% compared with control and changes in soil properties. The application of agricultural waste also significantly increased soil bacterial diversity, with the Shannon index increased by 2.37%–6.11% compared with control, and changed the bacterial community composition. The promotion of plant growth was linked with detectable shifts in the soil bacterial taxa after pre‐flooding and B. velezensis containing agricultural waste usage. Most importantly, random forest and correlated analyses showed that taxa affiliated with Pseudomonas may be important in strawberry growth after treatment. Subsequent bacterial isolation and pot inoculation experiments validated that co‐inoculation of Pseudomonas fluorescens and B. velezensis significantly promoted strawberry growth by 21.7% and 31.4%, respectively, compared with inoculation of only P. fluorescens or only B. velezensis, thus confirming the beneficial effect on strawberry plant growth in continuous cropped soils. Our results also indicate that co‐culture of P. fluorescens and B. velezensis could enhance biofilm formation and rhizosphere colonization, which may be essential in promoting plant growth. B. velezensis containing agricultural waste could stimulate indigenous Pseudomonas and promote plant growth by enhancing biofilm formation and rhizosphere colonization.