Legumes are one of the major sources of carbohydrates however proteins for human consumption however, so far, metabolomics studies remain limited to model species only. The Fabaceae family produces a plethora of structurally and functionally diverse metabolites, including biochemical compound classes which are has specialized metabolites and synthesized in response to biotic and abiotic stresses. There is a need to understand these molecular and biochemical mechanisms involved in the response of these crops to both stresses. Especially concerning the adaptive responses of legume species to both stresses as well as to point out the key primary and secondary metabolites involved in the adaptation and sensing mechanisms. Hence, in this review, legume metabolomic studies in response to biotic and abiotic stress have paved the way in understanding stress-signaling pathways. It aims to provides a progress update on metabolomic studies of legumes in response to different stresses. Moreover, metabolome annotation and data analysis platforms are discussed together with future prospects. This review will provide insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants