Nanotechnology is playing an increasingly important role in modern agriculture, as it offers new opportunities to improve the efficiency and sustainability of agricultural systems, promoting food security. The role of nanomaterials (NMs) as biostimulants in plants has been demonstrated through numerous investigations. The application of NMs to plants can induce positive changes in the metabolism, composition, and nutraceutical quality of the plants, as well as their tolerance to stress or toxicity. The interaction between the surface charges of NMs and plant cells leads to a sequence of events of perception, transduction, signaling, effector action and modification of genetic expression, which modifies metabolism or cellular characteristics. However, at the molecular level, there is little information on the changes in gene expression induced by NMs in plants. The objective of this review is to describe the impact of NMs as biostimulants in plants from the perspective of the analysis of the transcriptional response (changes in gene expression), which will provide a greater understanding of the molecular mechanisms involved in plant cells exposed to NMs.