The advancement of nanotechnology extends its investigation to diverse industrial and domestic domains. The escalating utilisation of nanomaterials (NMs) contributes to the potential threat of environmental pollution. NMs accumulate in plants, causing a danger to the ecosystem. The functional capacity of NMs is influenced by a variety of factors, including their chemical composition, size, surface coating, conjugation, and reactivity. This implies that their interaction with the plant is contingent on their physical and chemical characteristics. Chemical interactions involve the generation of reactive oxygen species, alteration of ion transport across the cell membrane, oxidative damage, and lipid peroxidation. It is possible that these particles may have a detrimental effect on plant development, as certain nanoparticles (NPs) are absorbed by the roots and transported through the vascular system, based on their structure, geometry, dimension, and physiology. These NMs reduce seed germination and root growth, as well. These NMs reduce seed germination and root growth, as well as causing a change in the root structure. Carbon-based NMs, such as fullerenes, carbon nanotubes, graphite, and nanofibres, are commonly employed as organic nanomaterials for the protection of plants under abiotic stress. The phytotoxicity of these NMs depends on their components and the type of usage they are intended for. Plants react to different environmental stress stimuli and their response is expressed through the production of proteins in specific cells or tissues. Adsorption of proteins on the surface of the nanoparticles, resulting in a protein-corona, alters the biological characteristics and behaviour of the nanoparticles, such as their permissibility inside the cell. Proteins, such as acuaporins, and those involved in the synthesis of ATP, are associated with transmembrane transport and exert an impact on the absorption of NPs or pollutants. The relevance of proteomic technology is that it helps us understand the mechanisms of response to stress in plants, such as the modification or generation of new proteins. This chapter delves into the current advancements in the toxic effects of carbon-based NMs on crop plants and explains how they respond to adverse environmental stimuli through the production of proteins.