A key challenge for the future, biorefineries are challenged by supply and demand variability. Indeed, biorefineries structures are traditionally centralised, with static processes where inputs and outputs are strictly defined and cannot be adapted (regarding quantity, quality, purity, etc.). This paper proposes a new approach where the process is decentralised to face the challenge of the agility of biomass processing. It leads defining virtual biorefineries, in which the stakeholders (farmers, industrials) are involved in a collaborative process, where they provide operation units as services and where existing plants and equipment are reused. The design of this collaborative biomass processing should also take into account functional and non-functional factors, such as the socio-economic context, weather conditions, etc. supported by information and communication technologies. Therefore, the biomass treatment process could be quickly designed and adapted, according to the detected changes of the ecosystem.