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Sustainable pest management is vital for promoting agricultural productivity while preserving environmental health. This study investigated the integration of plant-based pest control methods with environmental DNA (eDNA) metabarcoding to develop eco-friendly pest management strategies. Soil, plant, and air samples were collected from organic, agroecological, and conventional farms across Bangladesh to analyze microbial and pest diversity. Plant extracts from neem (Azadirachta indica), garlic (Allium sativum), and tobacco (Nicotiana tabacum) were prepared and tested against Helicoverpa armigera under greenhouse conditions at concentrations of 10%, 25%, and 50%. eDNA metabarcoding results revealed that organic farms exhibited the highest microbial diversity (Shannon index = 3.87), while conventional farms recorded the highest pest species diversity (species richness = 27). Pest mortality rates were concentration-dependent, with neem extract at 50% concentration achieving the highest mortality rate (91.3%), followed by garlic (85.7%) and tobacco (78.5%). Additionally, the 75% concentration treatments showed slightly lower efficacy, suggesting potential phytotoxicity effects. Statistical analysis confirmed significant differences (p < 0.05) between treatments and controls. The findings demonstrate that integrating eDNA-based biodiversity monitoring with plant-derived pesticides offers an effective, sustainable approach to pest management. This strategy can reduce reliance on synthetic chemicals, promote farm biodiversity, and support long-term agricultural resilience.