The process which includes production, gathering and transformation of biomass into renewable fuels and then into energy (both electrical and thermal) involves a large number of decisions to select the most efficient plant layout. The aim of the paper is to develop a general model for the simulation of the entire process from biomass to energy production in order to identify optimal plant solutions with respect to the current scenario. First, the hypotheses which can be adopted for the development of a physics-based model are outlined and discussed. Then, the model is implemented in Matlab environment, by adopting a modular structure in order to reproduce different plant configurations. Secondly, a general objective function is identified. Finally, an early-stage application of the model for methane production from biomass through anaerobic digestion is reported.