Abstract Background The use of chemical fertilizers and pesticides and the farming without crop rotation may negatively impact the microbial community and the quality of the soils in ginger farm. It is important to improve soil properties to promote the healthy growth of ginger in ginger farm. Results We isolated and identified the pathogenic Fusarium ramigenum from infected ginger roots. We then isolated a new Bacillus paralicheniformis strain SYN-191 from the rhizosphere soil around healthy ginger roots, and showed B. paralicheniformis SYN-91 could inhibit F. ramigenum growth, degrade proteins, dissolve silicate, and decompose cellulose. SYN-191 treatment significantly improved the agronomic traits of ginger seedlings in healthy soil and continuous cropping soil. Furthermore, SYN-191 treatment restructured the microbial microbiomes in rhizosphere soil, including reducing the number of harmful fungi, such as Fusarium, and increasing the beneficial bacterial populations such as Bacillus and Pseudomonas. Field experiments showed that SYN-191 application increased ginger yield by 26.47% (P