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Microbial inoculants that integrate plant growth promotion, pathogen suppression, and pollutant degradation are central to sustainable agriculture. Here, we report the genomic and phenotypic characterization of Lysinibacillus capsici BCSIR-Raj-01, an endophyte isolated from citrus leaves in Bangladesh. The 4.62 Mb genome encodes 4,699 coding sequences and displays an open pangenome with loci linked to stress adaptation, xenobiotic degradation, and secondary metabolite biosynthesis. Genome mining revealed complete pathways for indole-3-acetic acid (IAA) production, siderophore biosynthesis, and phosphate metabolism, alongside gene clusters for bacteriocins, lantibiotics, terpenes, and polyketides. Nitrogen cycling genes indicated diazotrophic growth potential and a truncated denitrification pathway. Phenotypic assays validated these predictions: L. capsici BCSIR-Raj-01 solubilized phosphate, produced IAA and siderophores, grew on hydrocarbons, and exhibited diazotrophic activity. Notably, the strain showed potent larvicidal activity against Culex and Anopheles larvae, suggesting ecological roles beyond plant association. Together, these results establish L. capsici BCSIR-Raj-01 as a multifunctional bacterium with potential applications in crop improvement, bioremediation, and biological vector control. The challenges of modern agriculture and environmental sustainability demand microbial solutions that deliver multiple functions. Lysinibacillus species are increasingly recognized for such versatility, but their genomic basis remains poorly resolved. Our study provides the first genome-enabled framework for understanding multifunctionality in L. capsici. By combining whole-genome sequencing with phenotypic validation, we show that BCSIR-Raj-01 harbors biosynthetic clusters, stress adaptation loci, and xenobiotic degradation genes while also expressing experimentally confirmed traits, including phosphate solubilization, IAA and siderophore production, nitrogen fixation, hydrocarbon utilization, and larvicidal activity. This integration of plant growth promotion, biocontrol potential, and pollutant degradation positions L. capsici BCSIR-Raj-01 as a next-generation bioinoculant. Beyond broadening the functional scope of Lysinibacillus, our findings highlight how genome-guided approaches can identify microbes with cross-sectoral applications in agriculture, bioremediation, and vector management.