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Recent economic pressures have forced the Australian sugar industry to achieve better integration and optimization of the cane harvesting and transport sectors of the value chain. The logistical and economic complexity of the harvesting and transport system was captured through the development of a modelling framework that effectively links several component models that describe the parts of the system. Through engaging in participatory research with representatives of a sugar region located at the north-east coast of Australia, we use this modelling framework to address some key industry issues in rationalizing rail track infrastructure and re-organizing harvesting. These issues were addressed by building component models for the modelling framework in the field of location science, namely the capacitated P-Median problem and spatial clustering. By applying the modelling framework and its component models to the case-study region, we explored a range of scenarios with a net cost reduction of up to AU$2260 000 per year. doi: 10.1057/palgrave.jors.2602024 Keywords: agriculture; strategic planning; location; transport