Intensification of agricultural practices has been pivotal in meeting the nutritional demands of a burgeoning global population. However, the widespread application of nitrogen (N) fertilisers has contributed to environmental pollution. In this study, we quantitatively assessed the role of international crop trade in optimising the productivity of micro-nutrients and its implications for N fertiliser use. Using a comprehensive dataset spanning from 1961 to 2019, we analysed the trade flows of seven key micro-nutrients—vitamin C (VC), vitamin B3 (VB3), vitamin B6 (VB6), calcium (Ca), magnesium (Mg), iron (Fe), and zinc (Zn)—embedded in agricultural products. We developed a novel framework to evaluate trade optimality and functionality based on the concentration-weighted productivity of micro-nutrients per kilogram of N fertiliser. Our findings reveal that while international trade has generally contributed to enhancing micro-nutrient productivity per unit of N fertiliser, trade optimality has shown a decreasing trend. High-productivity countries tend to export less relative to their potential, whereas countries with lower productivity import a larger share of crops. This decoupling suggests the need to re-evaluate trade policies to ensure that they align with sustainable agricultural practices and environmental conservation goals. We also identified potential savings in N fertiliser use through optimised trade practices, with estimated savings of 15–45 Tg of N per year. This could mitigate the negative agricultural impact and demonstrates the significant role that trade can play in achieving global sustainability targets. Overall, our research underscores the importance of aligning international crop trade with sustainable N management strategies to enhance micro-nutrient availability, improve environmental outcomes, and contribute to global efforts in achieving the Sustainable Development Goals.