Nanomaterials (NMs) have emerged as transformative tools in agriculture, offering novel solutions to enhance soil health, improve crop productivity, and manage plant diseases with precision. This review explores the biochemical, physiological, and molecular responses of plants to NMs, emphasizing their role in nutrient uptake, stress tolerance, and overall plant health. The integration of nano-fertilizers, nano-pesticides, and nano-sensors has demonstrated significant improvements in plant growth and yield, primarily due to enhanced nutrient efficiency and targeted pest control mechanisms. However, concerns remain regarding the long-term ecological and environmental impacts of NM applications, necessitating further research and regulatory frameworks to ensure sustainable usage. Biotechnological advancements, particularly in proteomics, have provided insights into NM–plant interactions at the molecular level. Proteomic studies reveal substantial alterations in protein expression and post-translational modifications that influence plant metabolism, photosynthesis, and stress responses. The potential of NMs to mitigate abiotic stresses such as drought and salinity through modulation of antioxidant enzyme activity highlights their promise for improving agricultural resilience. Despite these benefits, knowledge gaps persist regarding the dose-dependent effects of NMs, their bioaccumulation in plant tissues, and their impact on microbial ecosystems. To address these concerns, this review underscores the necessity of developing environmentally friendly nanotechnologies that optimize plant performance while minimizing risks. Future research should focus on integrating multi-omics approaches, refining application methods, and establishing comprehensive risk assessments to balance productivity with ecological safety. By leveraging advanced proteomics and nanotechnology, sustainable agricultural practices can be enhanced, contributing to food security and environmental conservation.