Ecological and soil physiochemical parameters impact the crop quality and development. In spite of the huge commercial prospective, the phytonutrient and chemometric profiles of Himalayan oregano (Origanum vulgare L.) have not been evaluated, and their relationships with ecological parameters are still lacking. The objective of this research study was to evaluate the disparity in the phytonutrient profiles of different ecotypes of O. vulgare in wild and cultivated populations and determine whether such variation was related to the diverse climatic and edaphic conditions prevailing in the northwestern Himalayas. Micrometeorological, atomic absorption spectroscopy for micro-elemental analysis was determined for soil. HPLC was used to determine the disparity in phytonutrient (quercetin, betacarotene, ascorbic acid, and catechin) and phytochemical (arbutin) levels. Cultivated populations had lower phytonutrient levels than wild populations. The habitat exhibiting pH values ranging from 6 to 7 elevated organic carbon (2.42%), nitrogen (97.41 kg ha-1), and manganese (10-12 μg g-1) and zinc contents (0.39-0.50%) show luxirant growth of Origanum vulgarel. The phytonutrient (quercetin, betacarotene, ascorbic acid, arbutin, and catechin) levels had a direct relationship with UV-B flux (r2 = 0.82) and potassium (r2 = 0.97). Wild accessions predominantly contained catechin and ascorbic acid, with maximum values of 163.8 and 46.88 μg g-1, respectively, while the cultivated accessions had the highest level of arbutin (53.42 μg g-1). Maximum variation was observed in quercetin (114.61%) followed by β-carotene (87.53%). Cultivated accessions had less quercetin (0.04-1.25 μg g-1) than wild accessions (1.25-2.87 μg g-1). Wild accessions had higher phytonutrient values for catechin, β-carotene, and ascorbic acid while cultivated accessions had maximum values for arbutin. The correlation of environmental variables with phytonutrient levels paves the way for metabolomic-guided enhancement of agricultural practices for better herb quality.