Transcriptomics has emerged as one of the powerful tools for investigating the impact of nanomaterials on plants at the physiological and molecular levels. This chapter provides an overview of the various transcriptomic methodologies, integrating transcriptomics with other omics approaches and their applications in elucidating the complex interactions between plants and nanomaterials. RNA sequencing has revealed key effects of nanomaterials on plants, such as the modulation of genes associated with photosynthesis, stress responses, and hormone signaling. Single-cell transcriptomics has provided insights into the cell-specific responses to nanoparticle exposure, identifying changes in gene expression related to oxidative stress, metal detoxification, and defense mechanisms. Integrating transcriptomics with other omics has further enhanced our understanding of various molecular mechanisms underlying plant responses to nanomaterials, including regulating primary and secondary metabolism and the induction of stress tolerance. Transcriptomic studies have also shed light on the differential gene expression patterns and key regulatory pathways modulated by nanoparticle exposure, such as activating transcription factors and altering phytohormone signaling. Moreover, the chapter discusses the potential applications of nanomaterials in agriculture, such as crop improvement and stress tolerance enhancement, as well as the challenges associated with their use, including toxicity assessment and regulatory concerns. Further, it emphasizes integrating transcriptomics with artificial intelligence and machine learning approaches as promising avenues for predicting nanomaterials’ effects on plant health and the environment, facilitating the development of eco-friendly nanomaterials for agricultural applications.