Background: Apple replant disease (ARD) is a common occurrence in many major apple-growing areas worldwide, seriously hindering the development of the apple industry. To avoid the shortcomings of chemical fungicides currently used to control ARD, it is necessary to find sustainable and effective control methods. Here, an endophytic phloridin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and its how to alleviates the pathogen pressure via changes in soil microbiomes were studied.Results: The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect reached more than 60%. The fermentation broth can also protect the roots of the plants from Fusarium infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and and indirect interspecific competition for nutrients. The antifungal organic compounds in the fermentation metabolites were identified using GC-MS technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate can promote the root elongation and lateral root development of Arabidopsis plants. The potential of strain XNRB-3 to control ARD was later validated using microbial fertilizer inoculation in pot and field experiment. The addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance (SOD, POD, and CAT) was also significantly enhanced. It also reduced the abundance of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as soil enzyme activity. Conclusions: The incorporation of strain XNRB-3 in the soil alleviated the damage of soil-borne pathogens to plants by reducing the relative abundance of pathogenic fungi and the content of phenolic acids, and inducing disease resistance of plants. Taken together, B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent. This provides a new management strategy to control ARD.