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Huanglongbing (HLB) pathogen <i>Candidatus</i> Liberibacter asiaticus (<i>C</i>Las) brings a great concern about the phloem nutrient transport in diseased plants. There is an urgent need to find the best management strategies to reduce the losses in the citrus industry worldwide. Endophytic bacteria are negatively affected by <i>C</i>Las pathogen, and these endophytes are associated with improved availability of nutrients and pathogen resistance. This study underpins the relationship between <i>C</i>Las pathogen, endophyte population and nutrients availability in citrus plants. The citrus plants were treated with <i>Bacillus subtilis</i> L1-21 and Hoagland solution to find out synergism efficacy to mitigate citrus HLB. We showed that citrus shoots in the presence of 50% Hoagland solution displayed maximum number of endophytes with 6.28 × 10³ to 3.04 × 10⁵ CFU/g. Among 50 candidate strains, <i>B. subtilis</i> L1-21 emerged as potential antagonist against surrogate strain <i>Xanthomonas citri</i> subsp. <i>citri</i>. The citrus half-leaf method identified that application of endophyte L1-21 with 50% Hoagland solution successfully reduces the <i>C</i>Las abundance. We point out that this combination results in a higher number of endophytes population with 2.52 × 10⁴ to 9.11 × 10⁶ CFU/g after 60 days, and reduces <i>C</i>Las pathogen abundance in asymptomatic HLB plants. In HLB symptomatic citrus plants, <i>B. subtilis</i> L1-21 potentially increases the endophyte population from 1.11 × 10⁴ to 5.26 × 10⁷ CFU/g in the presence of Hoagland solution, and pathogen abundance was reduced from 9.51 × 10⁵ to 1.06 × 10⁴ copies/g. Altogether, we suggested that the presence of endophyte L1-21 with Hoagland solution is more effective in HLB asymptomatic citrus plants, but a slight reduction of pathogen was observed in symptomatic plants. The findings revealed the role of indigenous citrus endophyte <i>B. subtilis</i> L1-21 along with other nutrients in the reduction of <i>C</i>Las pathogen abundance inside symptomatic and asymptomatic plants in citrus endophyte–nutrient–pathogen interplay.