Nano-based materials (NBMs) have special physicochemical properties, which offer them a wealth of opportunities in the field of agriculture. The interaction of NBMs with plants causes a variety of physiological, morphological, and genotoxic changes; understanding these effects is crucial for the efficient application of nanotechnology in agriculture. Researchers suggested that, depending on the properties of the NBMs, the mode of application, and species of the plant, there may be positive or negative impacts of NBMs on development and growth of plant. Recent research efforts involve in vivo studies in the field on the uptake, translocation, biotransformation, and risks of applying NBMs on the agricultural crops. In spite of the beneficial uses of NBMs in our daily life; however, their excessive usage at elevated concentrations displays deleterious effects; mainly phytotoxicity. NBMs induced phytotoxicity affects several aspects of the agricultural sector, including induction of oxidative stress, poor seed germination and reduced biomass yield, disruption of the photosynthetic machinery, alters gene expression, affects plant cell membrane integrity, causes damage to DNA, and elicits epigenetic variations in the affected plants. To understand comprehensively the physiological, biochemical, and molecular mechanisms of NBMs induced phytotoxicity, this review aims to study the various mechanisms of NBMs phytotoxicity, NBMs translocation and transfer within the root and leaves, effect on growth parameters (i.e., chlorophyll contents and total pigments) and yield of the plants, different defense mechanisms employed by the affected plants, induced deleterious molecular changes in the plant cell, and cell genotoxicity.