Nutritional stability – a food system’s capacity to provide sufficient nutrients despite disturbance – is a critical feature of sustainable agriculture, especially in light of ongoing climate change. Yet, measuring nutritional stability has proven challenging. Addressing this challenge will help identify resilient food systems, detect shortcomings in nutrient availability, and evaluate if stability-focused interventions actually work. We develop a novel approach that uses 55 years of crop data across 184 countries to assemble over 22,000 bipartite crop-nutrient networks. We then quantify the tolerance of these networks to disturbance simulated via sequential crop loss (Fig. 1) and evaluate patterns of crop diversity and nutritional stability across countries, over time and between crop supply scenarios (imports versus in country production). We observe a positive, saturating relationship between crop diversity and nutritional stability across countries; however there is substantial variability between countries over time. Next, despite crop diversity gains since 1961, nutritional stability has remained stagnant or decreased in all regions except Asia. A decline in the average number of nutritional links per network (range: -3 to -18% across regions) and the aforementioned saturating relationship explain this counter-intuitive finding. Finally, we find that imports increase crop diversity and improve or sustain stability, indicating that nutrient availability is market exposed in many countries, particularly developing states. Although applied globally, our approach is applicable across levels of organization, from household intake to sub-national production, and provides a way forward for understanding the contributions of crop diversity to the stability of nutrients available for human consumption.