The exploitation of neglected niger accessions plays a crucial role in future breeding programs aimed to enhance the quality. Present study evaluated the genetic variation in nutritional and nutraceutical compositions of 30 indigenous niger accessions originating from Eastern Ghats of India, and compare them with three improved varieties of the locality. The proximate compositions (g/100 g) showed significant variations, with moisture ranging from 1.36 g to 4.95 g, ash from 1.06 g to 5.45 g, fat from 28.53 g to 44.11 g, protein from 8.84 g to 18.18 g, carbohydrate from 11.21 g to 35.09 g, fiber from 16.32 g to 26.62 g, and energy from 407.32 Kcal to 526.84 kcal. Niger seeds are rich in phenol 41.10–82.20 mg/g, flavonoid 5.32–15.98 μg/g, antioxidant 13.59–31.08% across the accessions. Principal component analysis revealed that the first two axis explained 41.8% of the total variation, indicating significant differences among genotypes. The heritability and genetic advance in percent of mean (GAM) ranged from 61.11% to 99.91% and 12.5%–89.1% among the traits across the populations. High heritability and GAM recorded in vitamin C, ash content, antioxidant capacity, flavonoid and phenol suggests that these traits may be important for niger breeding program. Altogether, some indigenous niger accessions such as Mangardora, Ganjeipadar and Kolabnagar had exceptionally rich in fat, protein and energy contents and are nutritionally superior compared to improved variety of the locality. Further, exceptional rich in flavonoid, antioxidant capacity and vitamin C was recorded in Manahar, Badapada and Mahadeiput. These nutrition rich accessions have ample opportunities for future breeding programs aimed to enhance the quality and hold great potential in food industry for making high value functional food.