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Biohydrogen from endophytic fungi constitutes an alternative biofuel resource with considerable advantages over biodiesel and ethanol extracted from existing food crops. Endophytes common in plant tissues mimic host physiological behavior and produce primary and secondary metabolites like oils and fats. Therefore, endophytes from 7 selected 7 biodiesel plants, and 30 endophytic fungi isolated from 170 different plant parts were screened. The methodology included staining, lipid analysis, DNA isolation, molecular characterization, identification of fungal isolates by ITS sequences, biodiesel analysis, characterization of volatile organic compounds (VOCs), and statistical analysis. The fungal endophyte isolate SPSRJ28 was the most significant with an accumulation capacity of more than 20% of the total lipid content of its dry biomass, validating its oleaginous nature. In addition, the endophytes investigated in the present study yielded various VOCs that were validated by chromatography for both standards and isolates. When the VOCs were subsequently analyzed for their prospective usage as myco‐diesel, the presence of methane in the isolate SPSRJ28 was found to be highly significant. These findings remarkably support the investigation of endophytic fungi and their relationship with oleaginous plants as alternative sources of bioactive metabolites from microbial cell factories for myco‐diesel generation.