The present study is designed to determine the types of secondary metabolites in three selected seed powders by fast, reliable, and non-destructive Near Infra Red spectroscopic analytical technique. NIRS analysis of Macrotyloma uniflorum (Lam.) Verdc., Phaseolus lunatus Linn., and Phaseolus vulgaris Linn., seed flours were done for qualitative evaluation of secondary metabolites. The fine powder of crude drug was directly applied in FOSS XDS near infrared Rapid Content Analyzer. The properly filled powdered sample in a disposable glass silicate vial and closed with plastic lid was centrally placed onto the sample presentation glass of Foss Rapid Content Analyzer. The scanning of sample at ambient temperature gives NIR spectra within 30 seconds. The major proposed compounds in M. uniflorum were 3,4-dihydroxybenzoic acid, caffeic acid, chlorogenic acid, ferulic acid, gallic acid, kaempferol, linolenic acid, niacin, quercetin, sinapinic acid, syringic acid, and vanillic acid. Whereas, coumaric acid, fructose, galactose, L-serine, raffinose, stachyose, sucrose, threonine, and tyrosine were detected in P. lunatus and the NIR suggested the presence of caffeic acid, ferulic acid, sinapinic acid, phytic acid, leucine, and valine in P. vulgaris. NIRS as an advance innovative technology extensively used in chemical, food, petrochemical, and pharmaceutical industries for rapid and reliable standardization. The present study revealed a good correlation to conclude that flour samples of all the three legume seeds could potentially be added to food system to achieve nutritional and functional benefits.