Agri-food supply chains (AFSCs) lose approximately 1.3 billion tons of food annually, posing a major challenge to environmental sustainability. Logistics deficiencies are widely recognized as key drivers of postharvest losses. However, most studies examine isolated practices, with limited attention to their interactive effects across AFSCs stages, or to the mechanism linking operation practices, theories, and empirical research framework. This study conducts a systematic literature review following the PRISMA guidelines. Using Web of Science and Scopus, 90 empirical studies published between 2001 and August 2025 were analyzed to examine how food loss occurs and is mitigated across AFSCs. The review defines the operational boundaries of AFSCs, identifies six categories of food loss drivers, and systematically maps corresponding mitigation strategies across logistics stages. Findings indicate that logistics practices alone are insufficient to achieve effective food loss reduction. The effectiveness of logistics practices depends on organizational capabilities such as digital technology for monitoring and forecasting, collaboration for coordinated decision-making, and institutional pressures that encourage sustainable operations. Drawing on Natural Resource-based View, Dynamic Capability View, and institutional theory, this study proposes an integrated research framework to guide future empirical studies. The framework also provides practical guidance for managers and policymakers seeking to advance food loss reduction and contribute to achieving SDG 12.3.