When designing biomass-to-biofuel supply chains, the biomass uncertainty, seasonality and geographical dispersion that affect economic viability need to be considered. This work presents a novel methodology that can optimize the design of biofuel supply chains by adopting a decentralized network structure consisting of a mix of fixed and mobile processing facilities. The model considers a variable biomass yield profile and the mobile fast pyrolysis technology. The mixed-integer linear programming model developed identifies the optimal biofuel production and biomass harvesting schedule schemes under the objective of profit maximization. It was applied in the case study of marginal lands in Scotland, which are assumed to be planted with Miscanthus. The trade-offs observed between economies of scale against the transportation costs, the effect of the relocation costs and the contribution of storage capacity were investigated. The results showed that, in most cases, harvesting is most concentrated during the month of the highest biomass yield, provided that storage facilities are available. Storage capacity plays an important role to widen the operational time window of processing facilities since scenarios with restricted or costly storage resulted in facilities of higher capacity operating within a narrower time window, leading to higher investment costs. Relocation costs proved to have a minor share in the total transportation costs.