Bioactive compounds can be obtained from different sources and methods since various plants and microorganisms can synthesize them. There is also a wide variety of methodologies for their production, where the isolation of these compounds is the most important stage. Medicinal plants are one of the most used sources for obtaining bioactive compounds of natural origin due to their high content of essential oils made up of volatile and aromatic compounds that largely belong to the group of terpenes. Bioactive compounds of natural origin play a very important role in agriculture since they can combat many diseases caused by biotic and abiotic factors. Among the most important factors are phytopathogenic microorganisms such as fungi and bacteria, which cause yearly losses worldwide. In addition to being effective against plant diseases, bioactive compounds help search for alternatives to chemical pesticides, which can harm health and the environment and represent great costs for producers. In this way, bioactive compounds of natural origin could be used as biopesticides, representing a great alternative within the integrated management of plant diseases.