The fungal entomopathogen Beauveria bassiana could be established as an endophyte within jute (Corchorus capsularis) plant through seed inoculation. The highest colonization was observed in ITCC 6063 followed by ITCC 5562 and ITCC 5408 which are statistically at par (p < 0.05). The lowest apion infestation was observed in ITCC 5408, ITCC 6063, ITCC 4512 and ITCC 4563 which are statistically at par (p < 0.05). Highest apion infestation was observed in case of two non-endophytic isolates ITCC 4644 and ITCC 4925. Transcriptome study showed that a significant number of stem-weevil (Apion corchori) resistant genes involved in biosynthesis of plant volatiles viz., oxidative cleavage of fatty acids, LEGO-like building blocks, salicylic acid activation pathway, methyl jasmonic acid synthesis pathway were activated in ten B. bassiana isolate treated plants. RNA Sequencing was used to identify 1017 DEGs between ‘endophyte colonised plant’ and ‘untreated plant’. 1117 genes were up-regulated and 279 genes were down regulated in treated plant.