Highlights • Secondary metabolites are used in pharmaceutical industries, cosmetics, dietary supplements, fragrances, flavors, dyes, etc. • Metabolic engineering is an important biological tool to produce commercially importance metabolites. • The biosynthetic pathways for production of secondary metabolites in plants are derived from the shikimate, terpenoid, and polyketide pathways. • A huge number of medicinal plants and their metabolites have been produced by in vitro techniques.