Indonesia's food security landscape is influenced by various overlapping vulnerabilities, including climate change, recurring natural disasters, and institutional fragmentation. This study maps and analyzes the institutional frameworks governing food security in three crisis-prone regions (Aceh, East Nusa Tenggara (NTT), and South Sulawesi) using the Interpretive Structural Modeling (ISM) approach. Data was collected through expert interviews and focus group discussions involving representatives from 14 key institutions in Aceh Province, East Nusa Tenggara, and South Sulawesi, consisting of government agencies, private entities, and community-based organizations. The results of the study show that national institutions play a major role in improving food security in crisis-prone areas in Indonesia. Meanwhile, community-based and private institutions remain highly dependent and have limited influence in decision-making. The obstacles faced are damaged agricultural land and disrupted food distribution, causing price spikes and stock shortages in remote villages. Food production strengthening and agricultural insurance programs are urgently needed to maintain food security in disaster-prone areas. The changes that may occur through this program are the establishment of resilient local food systems in Aceh, NTT, and South Sulawesi provinces. These findings emphasize the importance of integrating top-down policy alignment with the strengthening of local institutions to build resilient and adaptive food systems. This model offers replicable analytical tools to improve food security governance in other contexts that are vulnerable to disasters and institutionally complex.