Cost optimisation in decentralised, make-to-order production systems requires tight integration with suppliers and transport operations as well as flexible network connections. Additionally, minimisation of environmental impacts of freight flows must be included in the industrial practice to realise sustainable growth. To these aims, the paper presents a model integrating production networks and sustainable freight transportation. The model includes Bill-of-Material constraints with alternative sources having different production and distribution costs. The objective function considers sourcing, production and transportation costs as well as environmental impacts of transport over a multimodal network. Due dates and time windows constraints for production and transportation management are included. Computational experiments are based on a real multimodal network. The optimisation model solved the case study instance. A sensitivity analysis proved the model robustness. The results demonstrate that the model can be effectively used in order to analyse cost-emissions trade-offs and the influence of links’ capacity on emissions.