In the field of plant biotechnology, what has attracted researchers’ attention is the use of nanoparticles due to their unique chemical and physical properties that can be helpful in the field of growth and development and improve the production of plant secondary compounds. Plant-derived metabolites have different biological and pharmaceutical properties which used in an extended range of industries, comprising food, cosmetics, and pharmaceuticals. Various factors such as environmental stresses, diseases, pests, the use of elicitors, and etc. can impact and restrict the yield and quality of secondary metabolites. The upcoming study focuses on the use of different nanomaterials in plant biotechnology and enhancing the production of secondary plant metabolites with a focus on biocompatible materials as efficient elicitors. Also, in this research, the physico-chemical properties of nanoparticles have been studied, factors that have made these materials attractive and suitable options for plant biotechnology. The mechanism of effect of nanoparticles in modulating the biosynthetic pathways of plant secondary metabolites as well as different types of nanomaterials used in plant biotechnology such as metallic and non-metallic nanomaterials and carbon nanoparticles are also presented in this review.