Bioactive compounds are produced by plants in huge quantities and are a valuable source for modern pharmacy, food additives, agrochemicals and cosmetics. For thousands of years, plants have been utilized in traditional medicines in different parts of the world. Research on plants has been substantially aided by the recent advancements in biotechnology in the areas of molecular biology, structural and functional genomics, highly efficient analytical chemical techniques and tissue culture. The present chapter is focused on the use of new advances in understanding the production of bioactive compounds in plants such as phenolics, alkaloids, flavonoids, terpenoids, tannins, glycosides, volatile oils etc. Although, these plant based products may have a similar upstream pathway that leads to a small number of common precursors but they differ in specific alterations that results in incredibly diverse structures. Understanding of the different pathways involved in biosynthesizes of these valuable compounds is essential for their large scale and cost-effective production, which in turn will not only improve human well-being but also conserve plant resources.