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There are numerous secondary plant metabolites found in the crop B. juncea, especially glucosinolates. Isothiocyanates, the by-products of glycosinolate breakdown, are beneficial to human health. A number of studies have also called attention to phenolic compounds and carotenoids, both well known for their anti-oxidant properties. A notable feature is that the profiles and concentrations of secondary plant metabolites vary greatly between varieties and that genetic factors are thought to be the most significant factors. In addition, environmental and agronomic factors have also been noted to change the concentrations of secondary plant metabolites. Secondary plant metabolites are primarily produced for defense purposes. Consequently, the intrinsic quality of Indian mustard, including color, aroma, taste, and medicinal properties, is profoundly influenced by its secondary metabolite profile. The health benefits of glycosinolates and the cancer prevention properties of their breakdown products make them of specific interest. Plant cells that have been injured undergo enzymatic decomposition of glucosinolate by endogenous enzymes such as myrosinase, which releases degradation products such as nitriles, epithionitriles, or isothiocyanates. The main phenolic compounds found in B. juncea are flavonoids and hydroxycinnamic acid derivatives. A diverse secondary metabolite pool is also essential for plant-environment interactions.

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