Abstract Food security is the major desired outcome of any food system, but its realization may be prevented by vulnerabilities in a food system. By shifting the focus of their vulnerability analysis from the discrete components of the food system to the food system as a whole, the authors of this article were able to develop a qualitative food system vulnerability matrix. The objective of the research was to make the concept of food system vulnerability operational by identifying vulnerability drivers, vulnerable systems and vulnerable subclasses in light of food security. The vulnerability matrix was set up with five classes of vulnerable systems (‘Vulnerability of what?’) on the horizontal axis and vulnerability drivers (‘Vulnerability to what?’) on the vertical axis. The authors analyzed the relationship between vulnerability drivers and vulnerable systems by using qualitative, abductive content analysis within the context of the Finnish food system. The data consists of public documents collected from the web pages of key organizations within the Finnish food system including ministries and their administration, interest groups and non-governmental organizations. It therefore covers various types of content related to food policy and management. Excerpts from the documentation data were coded according to which vulnerable system subclasses they addressed. The key findings of the study highlight the importance of using a systems approach that takes into account social, ecological and technical considerations. Such a framework covers multiple stressors, including exogenous natural drivers and endogenous social drivers, as well as the coalescence of vulnerability and food security discourses. The benefits of the proposed vulnerability framework for public food policy and food supply chain management include the explicit recognition of vulnerability drivers and vulnerable systems, a higher degree of specificity when speaking about food security, and opportunities for the identification of vulnerability-based innovations.