The agro-ecosystem, comprising crops and their environmental interactions, is significantly influenced by soil microbial diversity, which impacts soil and crop health. Monoculture practices, prevalent in India’s rice and wheat-based systems, degrade soil health and diminish microbial diversity by promoting selective microbial proliferation. Crop diversification is proposed as a sustainable alternative, enhancing soil health, microbial diversity, and resilience. By incorporating various crops, crop diversification improves nutrient cycling, soil structure, and organic matter content while reducing the need for chemical inputs. This holistic approach promotes biodiversity, pest control, and economic stability, contributing to more sustainable and resilient agricultural systems.