The interaction between plants and nanoparticles (NPs) is a fast-evolving field of study with scope for future advancement in agriculture, environmental remediation, and biotechnology. Depending on their mode of action, nanoparticles may affect plant physiology and development both at the molecular and cellular levels as well as at the whole-plant level. They may help induce growth and better nutrient uptake, along with stress resistance, although there is considerable emerging disquiet with respect to their toxicity and environmental impact. This chapter thus dwells on the molecular basis of how nanoparticles interact with and are taken up by plants, their translocation, and biotransformation within plant tissues. We elaborate on how surface properties, dimensions, geometry, and chemical composition of nanoparticles modify plant responses, welcoming the latest insights from genomic, transcriptomic, and proteomic studies, and the last are focused on some aspects namely effects on plant hormone signaling, reactive oxygen species (ROS) generation, and gene expression regulation. We also discuss some current problems and challenges, such as the standardization of experimental protocols and the mechanisms of nanoparticle translocation in plants. Finally, we talk about future directions, highlighting the practicalities of recombinant nanoparticles in enterprising agricultural technology and the responsible design of nanomaterials to minimize ecological impact. Thus, the chapter provides a general overview providing molecular understanding and guiding future research aiming at exploiting nanoparticles in plant science innovations.