Long harsh winter at the high-altitude reduces the cropping season to few months. So availability of fresh food is a major challenge at the high-altitude. Moreover vegetables imported from other regions (i.e., low-altitudes) may degrade in the nutritional quality, due to the long-transportation and logistic constrains. Keeping a view on the health-promoting qualities of onion (Allium cepa L.); the morphological, biochemical, and phytochemical profiling was studied in onion grown at high-altitude (3340 metres above mean sea level, Leh-Ladakh, India) with the lower-altitude (321 metres above mean sea level, Chandigarh, India). Higher-altitude cultivation resulted in better yield (32.55 ± 1.33 t/ha). Total soluble solid (10.62 ± 0.08 0B), crude protein (6.86 ± 0.10 g/100g), crude fat (0.17 ± 0.01 g/100g), total carbohydrate (93.78 ± 0.67 µg/g), nitrate (180.54 ± 7.77 mg/kg), sulphate (202.77 ± 2.95 mg/kg), nitrogen (1098.03 ± 15.26 mg/100g), sodium (97.05 ± 2.63 mg/100) and manganese (3.91 ± 0.05 mg/100g) contents were found higher at high-altitude whereas, phosphate (1058.27 ± 17.6 mg/kg), magnesium (150.68 ± 0.84 mg/100g), zinc (2.63 ± 0.04 mg/100g)), copper (2.32 ± 0.13 mg/100g)) and iron (16.56 ± 0.24 mg/100g) contents were found higher at low-altitude. Total phenolic (TPC) (5.93 ± 0.06 µg/mg), total flavonoid (TFC) (10.52 ± 0.13 µg/mg), quercetin (0.43 ± 0.01 µg/mg), anti-oxidant potential as indicated by ferric-reducing antioxidant power (FRAP) (42.27 ± 0.10 µg/mg) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) (43.22 ± 0.14%) content were higher in high-altitude grown onion bulbs. The high-altitude grown bulbs were found more effective in vegetative growth, yield and health promoting biochemical and phytochemical compound in comparison with low-altitude grown bulbs.