The population of the world is increasing rapidly, and it is challenging to fulfill the nutritional requirements of an overpopulated world. Therefore, it is necessary to identify underutilized food alternatives that are nutritious, have health-promoting properties, and are widely available. Seeds of mango, drumstick, and jamun are reported to have immense health promoting constituents. Despite this, they are largely discarded as waste due to lack of knowledge about their nutrient profile. Therefore, the present study aims at demonstrating the potential of nondestructive, rapid, and label free spectroscopic probes: attenuated total reflectance Fourier transform infrared spectroscopy, confocal micro Raman spectroscopy, and synchrotron radiation based X-ray fluorescence for determining the phytochemical and elemental profile of the mango, drumstick, and jamun seeds. The infrared and Raman spectra show that these seeds are rich sources of cell wall polysaccharides, amino acids, carbohydrates including glucose and starch, fatty acids, and antioxidants such as carotenoids and flavonoids. In addition, the X-ray fluorescence spectra show that these seeds are rich sources of calcium, potassium, magnesium, iron, copper, zinc, and manganese. The study highlights the potential of the nondestructive spectroscopic probes for the rapid, sensitive, cost effective and accurate assessment of nutrient profile of the seeds. The spectral information is highly beneficial for the administrators and nutrition scientists for assessment of diet quality, tackling malnutrition in an effective manner, and exploring use of these seeds.