The development of nanotechnology in agriculture has fuelled the rise of nanonutrients as prospective agents to improve nutrient use efficiency, crop yield and environmental sustainability. In contrast to traditional fertilisers, nanonutrients offer targeted delivery, slow release and enhanced absorption due to their nanoscale size and distinctive physicochemical properties. This review critically assesses the existing knowledge on nano-nutrient uptake, assimilation and translocation in plant systems. It emphasises the intricate interactions between plant physiological pathways and nanomaterials, including entry modes through leaves and roots, transport mechanisms at the cellular level and their ultimate distribution within plant organs. Additionally, this article provides a detailed account of the methodological strategies employed to investigate these processes. These methods include elemental and isotopic tracing, spectroscopic and molecular analyses, imaging technologies, physiological and biochemical assays, as well as dye-based tracking systems. The combination of these methodologies has enhanced our ability to quantify, visualise and comprehend the fate of nanonutrients in planta. Synthesising recent breakthroughs and methodological updates, this review aims to establish a foundation for future studies that maximise nano-fertiliser design and ensure their safe and efficient deployment in sustainable agriculture.