<p>This study develops a profit-oriented optimization model for a fresh agri-food e-commerce supply chain to address the limited integration of economic performance and environmental considerations in multi-echelon supply chain planning. The proposed system consists of multiple farmers, processors, distributors, and online customers for perishable products. A mixed-integer linear programming (MILP) model is formulated to maximize the total profit while explicitly accounting for carbon emissions and food waste generated from production, cold storage, transportation, and disposal activities. The applicability of the proposed model is demonstrated through a real-world case study of a fresh agri-food e-commerce network in Java Island, Indonesia. Computational results indicate that market store sales dominate total revenue, while online channels contribute a smaller but growing share. Sensitivity analysis reveals that demand and selling price fluctuations significantly influence total revenue, operational costs, profit, food waste generation, and carbon emissions. These results can assist managers in making optimal decisions regarding agri-food supply, production, and inventory that impact strategic, tactical, and operational policies.</p>