Agriculture, the primary source of human food, faces sustainability threats due to the complex interplay of political, social, and environmental factors, as well as the rapid technological advancements of the current era. Therefore, this study examines the effect of e-commerce adoption and carbon emission reduction on green supply chain performance in sustainable agri-food businesses. Carbon emission reduction is also used as a mediator between e-commerce adoption and green supply chain performance. Our study also measured the moderating effect of the size of the enterprise on the relationship between e-commerce adoption, carbon emission reduction, and green supply chain performance. We further developed a synthesized research framework based on resource-based view theory and existing literature. The 634 participants' data on e-commerce adoption, carbon emission reduction, and green supply chain performance were collected from the representatives of the target population using a 22- item survey questionnaire. Partial least square structural equation modeling (PLS-SEM) was used to measure the direct and indirect effects. Our results revealed that e-commerce adoption and carbon emission reduction have positive and significant effects on green supply chain performance. Results also proved that carbon emission reduction has a positive and significant mediating role in the relationship between e-commerce adoption and green supply chain performance. Moreover, results indicated that the size of the enterprise has no significant effect on the relationship between e-commerce adoption, carbon emission reduction, and green supply chain performance. Furthermore, it was concluded that e-commerce adoption and carbon emission reduction amplified green supply chain performance. Mediation clarifies its role in strengthening the relationship between e-commerce adoption and green supply chain performance in sustainable agri-food businesses. Findings provide valuable implications for policymakers and strategic management to promote e-commerce adoption in agri-food business firms.