Background Phloem limited non-culturable bacteria Candidatus Liberibacter asiaticus (CLas) affects the worldwide citrus production through causing citrus Huanglongbing (HLB). Despite the efficient colonization of citrus endophyte in the phloem as same niche as CLas pathogen, citrus microbiome manipulation and recruitment as well as citrus defense mechanisms in the presence of indigenous citrus endophyte against this pathogen are still unknown.Results Endophyte-mediated microbiome manipulation may potentially play a significant role in restoration of disease suppressive endophytic microbiome in vascular pathogen affected diseased plants and positively influence the citrus defense. For this, citrus endophyte Bacillus subtilis L1-21 was introduced in CLas-infected citrus groves for one year and pathogen reduction from 105 to 10 copies/gram/leaves was recorded. Resident bacterial community composition in diseased host dramatically changed after introduction of B. subtilis L1-21 and positive enrichment of certain bacteria was recorded in diseased citrus host. These enrichments were predominantly driven by high and low relative abundance of Bacillus and CLas pathogen respectively, after one year of endophyte application. Moreover, endophyte application resulted in citrus defence gene induction against CLas pathogen and demonstrated key resistance genes (PR-1, PR-4, RPS5, RBOHD) in endophyte-pathogen interaction pathway in infected citrus. Upon introduction of B. subtilis L1-21 in the diseased citrus plants, we identified high level of up-regulated genes (> 2-fold) involved in defense pathway (padj < 0.05) underpinning the fundamental defense mechanisms.Conclusion Thorough evaluation of disease suppressive mechanism of endophyte against pathogen requires further exploration. However, introduction of B. subtilis L1-21 restructured citrus microbiome by regulating key bacterial communities which might help plant to control this pathogen. In addition, we highlight advanced insights regarding activation of multiple disease resistance and secondary metabolites encoding genes in endophyte treated HLB-infected citrus plants showing potential resistance against CLas pathogen. Conclusively, endophyte-mediated manipulation could play decisive role in restoration of microbiome to positively influence the citrus defense.