The element phosphorus underpins the viability of global and national food systems, by ensuring soil fertility, maximising crop yields, supporting farmer livelihoods and ultimately nutritional security of the global population. The implications of global phosphorus scarcity therefore have serious potential consequences for future food security, yet these implications have not been be comprehensively or sufficiently assessed at the global or national scales. This paper offers a new integrated framework for assessing the vulnerability of national food systems to global phosphorus scarcity—the Phosphorus Vulnerability Assessment framework. Drawing on developments in assessing climate and water vulnerability, the framework identifies and integrates 26 phosphorus-related biophysical, technical, geopolitical, socio-economic and institutional factors that can lead to food system vulnerability. The theoretical framework allows analysis of context-specific food system by examining impact due to exposure, sensitivity and adaptive capacity. The framework will also ultimately provide guidance for food and agriculture policy-makers, phosphate producers and phosphorus end-users (primarily farmers and consumers) to take action to reduce their vulnerability to this new global challenge.