The soybean stem Melanagromyza sojae (Zehntner) (Diptera: Agromyzidae) fly, a polyphagous pest poses a substantial threat to various plant species within the Fabaceae family. This pest is particularly notorious for its infestation of soybeans, burrowing into the stems throughout the crop’s life cycle, from germination to harvesting. The damage it inflicts manifests as distinctive zig-zag tunnels containing maggots or pupae, along with observable exit holes. These maggots feed on the cortical layers of the stem, and in severe cases, they may extend their damage to the taproot, ultimately leading to the death of the plant. Early stage infestations result in seedling mortality rate, contributing to a decreased number of healthy plants. The consequences extend to reduced pod and seed formation, with reported average yield losses ranging from 20% to 30% in soybean crops across different regions globally. Integrated pest management emerges as a pivotal approach, encompassing a comprehensive strategy that integrates biological, cultural, and chemical control methods. This holistic approach aims to efficiently manage pest populations. In this chapter, we provide a comprehensive overview of the Soybean stem fly on its lifecycle, infestation patterns, and the multifaceted strategies involved in its management.