Human society is currently facing a growing demand for forest resources, which causes overexploitation and endangers biodiversity. In this regard, it is important to be aware that 10% of trees across the world are used in traditional and modern medicine. South America has the greatest diversity, with 40% of tree species in the world. The aim of our review consists of the assessment of the state of the art of micropropagation through somatic embryogenesis of representative medicinal trees in South America and of targeting the tree species that should be prioritized for conservation plans. From a total of 23,631 tree species from Central and South America, 31 are extinct, 7047 are threatened, and 1434 are possibly threatened. In this sense, in order to conserve them, various strategies are applied both in situ and ex situ. The application of in vitro multiplication protocols represents effective ways both in conservation and in the sustainable use of resources in order to obtain secondary metabolites of interest. Somatic embryogenesis is a well-known method in woody multiplication. According to the VOSviewer analyses, very few studies were available concerning aspects of somatic embryogenesis in medicinal trees. From the 10 representative species selected in our study, somatic embryogenesis protocols were established for 3 species, only for conservation purpose, not for secondary metabolites production. The development of protocols focused on obtaining secondary metabolites of medicinal trees will allow for the obtainment of valuable plant material as a non-invasive alternative.