<p>Indian mustard is widely used in culinary applications because of its nutraceutical properties as an anti-inflammatory, anti-cardiovascular, anti-carcinogenic, anti-microbial, anti-diarrheal, &amp; anti-ulcer agent. It is also a valuable cash crop for edible/industrial oil production. An increase in the productivity of oil seed crops, including the widely used <i>Brassica juncea</i> (Indian mustard), is a priority, as the import of edible oils is steadily increasing to meet the ever-growing domestic demand. The present study investigated the effects of soil type on the secondary metabolite composition and concentration in mustard leaf and flower tissues. Different mustard varieties (Kala Sona and MJ-1 varieties) grown on the same kind of soil and a single variety of mustard (Pioneer 45S46 variety) grown under two different edaphic conditions presented significant variations in secondary metabolite composition as well as concentrations in leaf and flower tissues, as determined by GC‒MS analysis. Interactions between soil and plants, facilitated by secondary metabolites, can affect plant–insect relationships, which in turn can impact the productivity of mustard.</p>