SummaryNutritional benefits of legumes make them an important part of sustainable diets. They are rich not only in dietary fibres, proteins, and micronutrients but also in the bioactive compounds that can exhibit various biological activities. In the present study, we aimed to investigate the nutritional analysis, phytochemical composition, and in vitro anti‐obesity activity of two varieties of legumes indigenous to India namely, adzuki beans (Vigna angularis) and mung beans (Vigna radiata). GC–MS, UHPLC‐QTOF‐MS, ICP‐MS analyses were done for bioactive compounds, fatty acids, macro‐elements, micro‐elements, protein, and non‐proteinogenic amino acids. GC–MS analysis showed that the major constituents identified were hydrocarbons, fatty acids, and terpenes, while the presence of various secondary metabolites, macro‐ and micro‐nutrients were detected using UHPLC‐QTOF‐MS and ICP‐MS, respectively. FAME analysis revealed a higher concentration of linoleic acid in adzuki beans, which is nutritionally beneficial for human consumption. Amino acid profiling revealed the presence of essential, non‐essential, and non‐proteinogenic amino acids. Further, adzuki beans and mung beans were screened for cytotoxicity on 3T3‐cell line and it was observed that adzuki beans were less cytotoxic as compared to mung beans. Adzuki beans showed higher HMG‐Co‐A reductase enzyme inhibition activity (60%) as compared to mung beans (2.79%). The results indicate that these two legumes are a very good source of bioactive metabolites and can be developed into novel cholesterol‐lowering and anti‐obesity functional foods.