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Summary: Food security is a critical concern for emerging nations, where agriculture is a vital source of livelihood for a significant proportion of the population. However, ineffective food grain storage management (FGSM) poses a substantial threat to food security, resulting in significant post‐harvest loss (PHL). This research aims to identify and analyse the challenges to sustainable FGSM in emerging nations, with a specific focus on India using Total Interpretive Structural Modelling (TISM) and Matrice d'Impacts Croisés Multiplication Appliquée á un Classement (MICMAC) analysis. The study identifies 15 critical challenges after doing a thorough literature review, consulting with industry experts, and a dedicated questionnaire survey. The study finds that inadequate government policies and a lack of commitment from the top management are the major challenges to sustainable FGSM. The combination of the qualitative and quantitative model provides a comprehensive understanding of the identified factors and their interrelationships, offering a logical framework to support decision‐making and encourage sustainability. This paper contributes to the broader debate on sustainable food production and consumption by highlighting the importance of sustainable FGSM in emerging nations. [ABSTRACT FROM AUTHOR]