Entomopathogenic fungi are known to produce a multitude of low molecular weight secondary metabolites involved in different biological processes including fungal development, intercellular communication and interaction with other organisms in complex niches. In the present investigation, heterogeneity in metabolome profile of three isolates of Beauveria bassiana viz., MH590235 (TM), MK918495 (BR) and KX263275 (BbI8) were analyzed through GC-MS. Distinct differences in metabolite profile of the isolates were observed. A total of 63 metabolites were detected from all the isolates combined. Metabolites, 5-Oxotetrahydrofuran-2-carboxylic acid and undecane were found to be specific to BR isolate. Macrocyclic gamma lactones were detected in culture filtrates of BR and BbI8, oleic acid and hexadecanoic acid in TM and BR. An insecticidal compound, levoglucos an was detected in all the fungal isolates. Among the isolates, TM revealed higher variability in the metabolite production through PCA analysis. The metabolome of TM isolate contained compounds having several biological functions, viz., insecticidal and antimicrobial activity, lipid and fatty acid metabolisms and virulence enhancing factors.