This article presents an effective solution method for a two-layer, NP-hard sustainable supply chain distribution model. A DoE-guided MOGA-II optimiser based solution method is proposed for locating a set of non-dominated solutions distributed along the Pareto frontier. The solution method allows decision-makers to prioritise the realistic solutions, while focusing on alternate transportation scenarios. The solution method has been implemented for the case of an Irish dairy processing industry’s two-layer supply chain network. The DoE generates 6,100 real feasible solutions after 100 generations of the MOGA-II optimiser which are then refined using statistical experimentation. As the decision-maker is presented with a choice of several distribution routes on the demand side of the two-layer network, TOPSIS is applied to rank the set of non-dominated solutions thus facilitating the selection of the best sustainable distribution route. The solution method characterises the Pareto solutions from disparate scenarios through numerical and statistical experimentations. A set of realistic routes from plants to consumers is derived and mapped which minimises total CO2 emissions and costs where it can be seen that the solution method outperforms existing solution methods.