Macrophominaphaseolina is attributed to infect a wide range of plants. There are not a successful strategies to eradicate the fungus from the soil. In this study, a jute endophytic bacteria, Burkholderiacontaminans has been found to have a promising effect in controlling M. phaseolinain in vitro culture. Using the iTRAQ LC-MS/MS method for quantitative proteomics study, a comparative analysis of the whole proteome of M.phaseolinaunder both Burkholderiachallenged and unchallenged conditions were made and analyzed. A tough battle appears to ensue between the fungus and the bacterium, where Burkholderia manages to arrest the growth of the fungus and decrease its pathogenicity but, the latter apparently survives under ‘hibernating’ conditions by up-regulating its energy metabolism.