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Background Microbial biological control agents are gaining worldwide attention to manage insect pests as an alternative to synthetic insecticides. Entomopathogenic fungi (EPF) meet eco-friendly pest management’s demand since mere contact of infective propagules is sufficient to cause disease in insect pests, unlike other entomopathogens. However, epiphytic fungal isolates encounter multiple challenges including direct exposure of conidia to sunlight and UV light, high temperature, and low moisture content that reduce their efficacy at the field level. Therefore, utilization of endophytic EPF is becoming more popular because they get protection from adverse conditions compared to the epiphytic EPF as they reside inside the host tissue. In addition, the endophytic EPF also give protection against crop diseases and promote plant growth, degradation of heavy metals, and tolerance to abiotic stress. Results The increased mortality of Spodoptera litura (Fab.) (Noctuidae: Lepidoptera) was achieved through endophytic colonization of indigenous Beauveria bassiana UHSB-END-1 (OM131742). The bioassay proved the highest mortality 2nd instar larvae of S. litura at 40 dpi, both in vivo and in planta experiment. Further, larvae fed with fungal colonized leaves of tomato plant ended with abnormal growth and developmental process. The recovery of B. bassiana from different plant parts (stem, leaves, and roots) was the highest (100%) in all the methods of colonization at 14, 40, 60, 80 dpi, and it was decreased at 120 dpi (80%). The colonization rate was again increased in the next-generation seeds and seedlings (25 days old). This isolate gets vertically transmitted to their progenies via seeds, and it is the first report in tomato crop. Conclusion After ensuring the safeness of this isolate against non-target organisms, it can be one of the constitutes in sustainable cost-effective strategy for management of pests affecting tomato as one of the components in integrated pests management. Inoculation of endophytic EPF into seed/seedling reduces environmental impacts and also easy, economical, and sustainable approach for pest management in horticulture crops which are often consumed as raw. Although field studies are required to support the present finding, this appears to be an interesting tool that should be considered for pest biocontrol.