In this article, we design a multi-stage supply chain consisting of Suppliers, Distribution Centres, Branches and Customers, allowing multi-commodity product transfer to satisfy the end consumer demands. We take into account both fixed and variable emissions due to the operation and amount of goods transferred through the intermediary echelon-facilities of Distribution Centres and Branches, as well as during transportation. The decisions include whether to keep the intermediary echelon-facilities running during the planning horizon, and the product flow path from the Suppliers to the Customers through the functional intermediary echelon-facilities. We consider capacity constrained facilities and homogeneous vehicles, with the optimization goal of the green supply chain being the overall emission minimization. In addition to the green objective of emission reduction, we separately model fixed and variable supply chain costs similar to emissions, and estimate the emission trade-off when such cost minimization objectives are used. Further, we also consider the impact of supply chain integration on both of these objectives, with the same MILP being used on integrated supply chains for optimization; the process of integration of two or more supply chains involves coalescing each individual stage of the supply chains separately (e.g. all Branches across the supply chains being integrated are merged together to form a single set of Branches, and likewise) with additional new transportation links being provided for allowing the new transport pathways. We find that trade-off in emissions when using the cost objective (i.e. for efficient supply chains) is proportional to the size of the supply chain, and propose the introduction of a new classification strategy for environmentally friendly supply chains, that being of green supply chains with the fundamental objective being to minimize wastes and emissions. All codes to replicate the computational results, and synthetic datasets generated by us are hosted online.