Malaysia’s food industry is facing escalating pressure from rising population demands, resource scarcity, and the mounting effects of climate change. As agriculture remains vital to national food security and economic stability, managing its environmental footprint—particularly CO₂ emissions—has become an urgent priority. Despite growing global attention to sustainability, limited empirical research has explored how internal organizational dynamics and energy transition efforts influence emissions outcomes in the Malaysian context. This study aims to address this gap by examining the effects of agriculture industry operations, renewable energy consumption, and government initiatives on CO₂ emissions management, with organizational perception acting as a mediating factor. Using Partial Least Squares Structural Equation Modeling (PLS-SEM) on pilot survey data from food industry stakeholders, the findings highlight that organizational perception significantly mediates the relationship between renewable energy consumption and government initiatives on CO₂ emissions outcomes. While agricultural operations do not directly or indirectly influence emissions through organizational perception, both renewable energy use and proactive government policies foster a stronger environmental orientation within organizations—leading to improved emissions management. The study contributes to the discourse on sustainable development in emerging economies by emphasizing the critical role of organizational mindset in translating external sustainability drivers into tangible environmental outcomes. These insights offer practical implications for industry leaders and policymakers seeking to enhance sustainability strategies within Malaysia’s agri-food sector.