Industrial effluents in recent years have generated environmental problems that need to be addressed, leading to the search for environmentally friendly methods to eliminate persistent substances, such as organic pollutants that seriously affect the environment and human health. Recent studies have shown that microbial or plant secondary metabolites can be used for bioremediation. At the same time, it has been observed that the treatment of pollutants enables the production of value-added compounds important to other industries, such as the food industry. Various biotechnological techniques have been used to get them, which allows optimizing processes. At the same time, nanoformulations have been considered since they adequately resist the absorption of toxic compounds. This is why this chapter describes the secondary metabolites of interest for bioremediation, methods for obtaining them, and their formulation for application, highlighting how this approach favors the production of value-added compounds for other industries.