Soybean research has gained immense attention due to its extensive use in food, feedstock, and various industrial applications, such as the production of lubricants and engine oils. In oil crops, the process of seed development and storage substances accumulation is intricate and regulated by multiple transcription factors (TFs). In this study, FUSCA3 (GmFUS3) was characterized for its roles in plant development, lipid metabolism, and stress regulation. Expressing GmFUS3 in atfus3 plants restored normal characteristics observed in wild-type plants, including cotyledon morphology, seed shape, leaf structure, and flower development. Additionally, its expression led to a significant increase of 25% triacylglycerols (TAG) and 33% in protein levels. Transcriptomic analysis further supported the involvement of GmFUS3 in various phases of plant development, lipid biosynthesis, lipid trafficking, and flavonoid biosynthesis. To assess the impact of stress on GmFUS3 expression, soybean plants were subjected to different stress conditions, and the its expression was assessed. Transcriptomic data revealed significant alterations in the expression levels of approximately 80 genes linked to reactive oxygen species (ROS) signaling and 40 genes associated with both abiotic and biotic stresses. Additionally, GmFUS3 was found to regulate abscisic acid synthesis and interact with nucleoside diphosphate kinase 1, which is responsible for plant cellular processes, development, and stress response. Overall, this research sheds light on the multifaceted functions of GmFUS3 and its potential applications in enhancing crop productivity and stress tolerance.