Physicochemical and phytochemical assessment of leaf mustard (Brassica juncea L.) grown in different agroclimatic conditions is essential to highlight their compositional variability and evaluate the most suitable bunch of agroclimatic and agronomic practices. B. juncea is one of the important leafy vegetables that serve as source of vitamin A and C and iron, and plenty of antioxidants. This in situ research was executed to assess the quality variability of B. juncea grown in different agroecosystems. Leaves’ samples of B. juncea were procured from 15 farmers’ fields exhibiting different agroclimatic conditions i.e., elevation, nutrient management, temperature, irrigation, and tillage practices. Leaves’ samples were subjected to physicochemical and phytochemical analysis, i.e., moisture, pH, TSS, ascorbic acid, carotenoids, phenolics, flavonoids, and antioxidant potential. In the leaves’ samples of B. juncea, the target properties were found to vary significantly (P ≤ 0.05) in different agroclimatic conditions. The moisture content, ascorbic acid, phenolic content, carotenoids, and antioxidants were found in the range of 62.7–79.3%, 74–91 mg/100 g, 49.2–49.2 mg GAE/100 g, 436.3–480 mg β carotene/100 g, 32.7–46.67%, respectively. This study elaborates the significant variation of physicochemical and phytochemical attributes of B. juncea due to the prevailing agroclimatic conditions. This necessitates the appropriate choice of B. juncea concerning its composition and ecological conditions of its cultivation in the prospective health benefits.