<p>Traditional herbal formulation is widely used in natural farming, such as biopesticides for pest control and biofertilizers for enhancing the microbial activity, soil fertility, and sustainability for crop production. However, their microbial and metabolomic profiles and molecular mechanisms have not been scientifically reported. This study shows the integrative multi-omics characterization of Agniastra formulation and insecticidal activity against <i>Spodoptera litura</i> and <i>Spilosoma obliqua.</i> Metagenomic analysis revealed fermentation-based microorganisms mainly belonging to lactic bacteria, including <i>Lactipanibacillus</i>, <i>Aerococcus</i>, and <i>Weissella</i>, and unclassified taxa, showing the presence of unknown functional groups. LC-MS/MS and GC-MS/MS identified various bioactive compounds, including azadirachtin A, nicotinic acid, pyrethrin I, citral, and amino acid derivatives. Molecular docking showed a strong interaction of azadirachtin A with juvenile hormone epoxide hydrolysate and spinosyn A with chemosensory protein, which highlights the multi-target action potential of Agnistra biopesticide. In vivo bioassay showed larval mortality, with 46.66% mortality of <i>S. litura</i> and 53.33% mortality of <i>S. obliqua</i> after the first spray and 100% mortality observed in both larvae after the second spray. This study confirms Agniastra as a microbial-metabolite system showed laboratory insecticidal efficacy against <i>S. litura</i> and <i>S. obliqua</i>. Non-target safety and field efficacy require validation through standardized toxicity assay.</p> Graphical abstract <p></p>