As the integration of engineered nanomaterials into agriculture and industry expands, understanding their phytotoxic effects on plants and other economically important crops becomes increasingly critical. Flow cytometry has hence emerged as a vital tool in assessing the phytotoxic effects of these particles. The technique accounts for rapid, high-throughput in-depth analysis of various cellular processes impacted by nanoparticle exposure. It has been widely applied to measure cell viability, oxidative stress, apoptosis, autophagy, DNA damage, and changes in the cell cycle, amongst other applications. These insights are crucial for understanding the physiological and biochemical disruptions caused by nanomaterials. Through ongoing and continuous advances in instrumentation and analytical tools, flow cytometry continues to gain importance as a reliable method in nanotoxicology and plant-environment interaction research.