The consumption of medicinal plants has increased in recent decades due to the fact that they biosynthesize compounds with many biological activities; thus, some plant species with biological potential are being utilized as raw material by the industries for preparation of drugs, phytodrugs, or food supplements. This has the consequence of overexploitation and deforestation, which endangers plant species-of-interest. In recent years, alternatives have been sought to eradicate this problem. A solution that was given and is maintained is plant biotechnology, which favors the production of secondary metabolites (SMt) with important biological activity. Plant biotechnology allows us to increase the yield of a compound-of-interest, reduces its production times and costs, and allows constant and controlled production of the raw material, while aiding in the protection of medicinal plants that are found in danger of extinction. In the scientific literature, procuring the SMt by means of biotechnological processes is described, highlighting the study of five species from Mexican traditional medicine (Lopezia racemosa, Galphimia glauca, Cnidoscolus chayamansa, and Buddleja cordata), and the main biological activities are as follows: anti-inflammatory, hepatoprotector, neuroprotector, anxiolytic, antitumoral, antibacterial, and antioxidant, among others. KEY POINTS: • Secondary metabolites produce by biotechnology processes • Active secondary metabolites isolated from Mexican medicinal plants • Recent advances on the production of some bioactive secondary metabolites.© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.