The application of nanomaterials in plant biotechnology has turned out to be an innovative and promising idea to develop efficient methods to improve plant growth and increase the production of bioactive compounds such as alkaloids, flavonoids, phenolic acids, glycosides, among others, which are widely studied due to their high value in the food, cosmetic and pharmacological industries. In this sense, it has been seen that some nanomaterials, such as Cu, Ag, TiO2, ZnO nanoparticles and carbon-based materials such as carbon nanotubes, to mention a few, promote organogenesis and callus production in in vitro cultures; likewise, it has been reported that the use of nanomaterials induces important somaclonal changes, such as changes in metabolism, conferring improvements in survival and reproduction, and allowing the adaptation of plants to different types of biotic and abiotic stresses. On the other hand, it has been found that the application of nanomaterials as abiotic elicitors can increase the production of secondary metabolites in in vitro cultures, improving their availability and specificity. Based on the available studies, the framework of this chapter summarizes the use and impact of some nanomaterials on plant reproduction in vitro, the somaclonal variations that may occur, as well as their influence on the production of secondary metabolites, and their ability to adapt to different types of stresses.