The study of secondary metabolism in plants is an important source for the discovery of bioactive compounds with a wide range of applications. Today these bioactive compounds derived from plants are important drugs such as antibiotics, and agrochemicals substitutes, also this have been economically important as flavors and fragrances, dyes and pigments, and food preservatives. Many of the drugs sold today are synthetic modifications of naturally obtained substances. There is no rigid scheme for classifying secondary metabolites can be divided into different groups based on their chemical components, function and biosynthesis: terpenoids and steroids, fatty acid-derived substances and polyketides, alkaloids, phenolic compounds, non-ribosomal polypeptides and enzyme cofactors. The increasing commercial importance of these chemical compounds has resulted in a great interest in secondary metabolism, particularly the possibility of altering the production of bioactive plant metabolites by means of tissue culture technology and metabolomics. In today’s world the use of bioactive compounds derived from plants plays important roles in pharmaceutical applications. This review presents information about these metabolites and their applications as well as their importance in agronomy and bioactive effects on human health as nutraceuticals. Also this review includes the new tendencies to produce these bioactive compounds under different stresses conditions such as biotic and abiotic stress that could be included in production systems.