AbstractA decentralized supply chain that integrates biomass depots as an intermediate pre‐processing hub may be an efficient way to obtain stable and dense non‐food carbohydrate commodities that are economically transportable over long distances. This paper presents an integrated geographic information systems (GIS) method based on transport optimization to design and compare the performance of a decentralized versus a centralized biorefinery supply system. The method determines the suitable locations, allocations, sizing, and number of depots according to different demand location scenarios. The method is exemplified by a real case study in southern Quebec. In the design, the biomass depot generates raw sugar, shipped to the biorefinery, and co‐products that are used on site without transportation as animal feed and bioenergy. This diversification strategy provided by a joint production permits savings amounting to two‐thirds of the tonnage on the second transportation arc. The results present the average travel time performance in minutes in different scenarios. In the centralized configuration, the optimized stand‐alone biorefinery location scenario is 45% (59 min) and 58% (100 min) more efficient in terms of transportation than the two biorefineries located in existing industrial parks. However, the latter have a decentralized configuration that is more efficient than their centralized equivalents. In the decentralized configuration, depending on farmer participation, the biorefineries located in the existing industrial park have a transportation performance 16–42% (27–55 min) that is more efficient than their respective centralized configuration. Smaller depots and the use of numerous depots tend to reduce the average impedance as biomass availability increases. This is due to the economies of transportation related to a denser and more meshed network. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd