This paper analyses and compares regional food systems in Latvia and Lithuania from the perspective of sustainable food security and poses three questions: (i) what are the general food system characteristics and drivers of change in Latvia and Lithuania? (ii) how are the regional food systems constructed and performing? (iii) what are the conditions and pathways for regional food systems to become more sustainable? The paper examines in-depth the food systems in two regions – Pierīga region in Latvia and Vilnius region in Lithuania. The research is carried out within the framework of the EU projects TRANSMANGO and SALSA, and the Latvian Council of Sciences project SINFO. We find that food chain concentration and the interests of big food industries and retailers drive food systems in Latvia and Lithuania while civic and consumer-driven initiatives are becoming more important in stimulating a transition towards sustainable diets. The regional food systems are a complex intertwinement between the agro-industrial, proximity, domestic, and ecological subsystems. The pathways towards more sustainable regional food systems are difficult to negotiate and enforce as they require collaboration among various stakeholders who have different agendas. The long-term prospects of the regional food systems in terms of social and economic sustainability cannot be viewed in isolation from the demographic trends in the region, the steady depopulation in rural areas and efforts in strengthening urban-rural synergies.