Increasing global food demand, and risks associated with climate change and agrochemicals demand novel and sustainable agricultural practices to improve crop yield and quality. Various strategies using nanotechnology have been explored widely to provide solutions. However, their application in the food industry is constrained by limited understanding of nanomaterial safety. Growing interest in the potential of engineered nanomaterials (ENMs) in agricultural applications has also resulted in increased crop exposure, leading to unknown risks to plants, animals and humans. Recently, considerable research has been carried out on overt plant response to ENMs; however, conclusive mechanistic information is lacking. With advancements in hyphenated analytical techniques, research on ENM-biota interactions has witnessed a paradigm shift from low-throughput, single end-point bioassays to high-throughput, discovery-oriented omic tools, including transcriptomics, proteomics and metabolomics. This review summarizes the pioneering studies utilizing omics in plants exposed to ENMs to explain phenotypic expressions and elucidate associated biological pathways. Advantages and challenges of current analytical techniques employed in proteomics and metabolomics are also discussed. We acknowledge the need for integration and application of multiomics to identify sensitive biomarkers in plants in response to ENMs, and provide mechanistic insights, in order to design enhanced and safer nano-enabled products for agriculture.