Plants display an amazing biosynthetic capacity. To date, around 200,000 different chemical compounds have been isolated from them. Only a relatively few of these compounds are common to all plant species, since they are involved in basic or primary cell processes, such as energy metabolism. However, the broader plant chemical diversity corresponds to those compounds showing a restricted distribution among only a few taxonomically related species and which are not involved in primary metabolic pathways. These compounds are called secondary or specialized metabolites and they have important roles in numerous plant-environment interactions. Aside from these functions, secondary metabolites, and the plants bearing them, represent highly regarded commercial products given their pharmaceutical, flavoring, aromatic, coloring, and poisonous properties. In here, we present some selected examples of secondary metabolite-producing plants for which efficient protocols of somatic embryogenesis have been developed. The review covers mainly plants producing fine chemicals, used either in pharmaceutical or food industries. As shown, the development of somatic embryogenesis procedures could respond to two main goals: the genetic transformation of a given plant species, or the massive propagation of selected materials. Furthermore, the use of such protocols for the generation of diversity through indirect embryo formation is also presented.