High logistics and handling costs prevent the bioenergy industry from making a greater contribution to the present energy market. Therefore, a mathematical model, OPTIMASS, is presented to optimise strategic (e.g. facility location and type) and tactical (e.g. allocation) decisions in all kinds of biomass-based supply chains. In addition to existing models, OPTIMASS evaluates changes in biomass characteristics due to handling operations which is needed to meet the requirements set to biomass products delivered at a conversion facility. Also, OPTIMASS considers the re-injection of by-products from conversion facilities which can play a decisive role in the determination of a sustainable supply chain. The scenario analysis illustrates the functionalities of OPTIMASS in the optimisation of an existing supply chain, the definition of the optimal location of new conversion facilities and the definition of the optimal configuration of a supply chain. OPTIMASS, as a deterministic model, does not consider variability related to e.g. seasonal changes which can be a major obstacle. However, a thorough sensitivity analysis of influencing factors must give insight in the induced changes in the supply chain. The sensitivity analysis in this paper investigates the influence of uncertainty in biomass production, energy demand and of changes in transport distance. The analysis demonstrate that OPTIMASS can be used as an inspiring tool to investigate the possible effects of governmental decisions, of considering new biomass material, new facilities, of technology changes, etc. The coupling with GIS allows characterisation and visualisation of problems in advance and visualisation of results in an interpretative way.