Characterizing food systems, i.e., describing their organizational features, can help to generate a better understanding of the structural vulnerabilities that constrain transitions towards sustainable food security. However, their characterization across different economic contexts remains challenging. In this paper, by linking key concepts from research on food regimes, food system vulnerabilities and responsible innovation, we aim to characterize food systems in a developing and a developed economy to identify their shared vulnerabilities. We applied a case study design to characterize food production, processing and distribution in the province of Québec (Canada) and in the state of São Paulo (Brazil). In both cases, the processing and distribution stages have higher economic predominance when compared to the agricultural production stage. Furthermore, we observed concentration in a few activities in both food systems, with a shared focus on export-oriented supply chains. Vulnerabilities in both food systems include: (1) increased interdependence because some supply chains are export-oriented or depend on foreign labor and are, therefore, exposed to external risks; (2) concentration in a few activities, which threatens present and future local food diversity and (3) unequal power relations, making small and medium players vulnerable to decisions made by big players. The characterization developed in this study shows that the two food systems are mainly pursuing economic goals, following the institutional logics of the neoliberal food regime, which are not necessarily aligned with food security goals. It also exposes the presence of characteristics of ‘responsibility’ that may eventually help overcome food systems' vulnerabilities and support transitions toward sustainability.