This article presents the results of an ongoing research project on production and allocation of the biomass of agricultural origin (BAO), a key resource in ecological and energy transitions. The production and allocation of BAO are changing under the current development of the bioeconomy, which is the narrative promoted for intensifying the use of BAO, that we question through the lens of the scientific paradigm of bioeconomics. We developed a metabolic approach to agriculture, that we applied to the case study of northern Aube (France), an area specialized in intensive crop farming, undergoing rapid development of agricultural biogas production. Our results indicate that the ongoing changes influence BAO production and allocation at several scales (farm, small collective of farms, value chain, territorial). Development of the bioeconomy strongly influences the socioeconomic metabolism of the territory’s agriculture. Diversion of BAO flows due to biogas production are increasing structural imbalances and have some negative impacts on flows and ecological or economic funds strategic for sustainability, agronomic and economic balances of agricultural activities at multiple scales and as a whole. The changes described are especially disruptive since they strengthen competition and have blocking effects for the existing and potential agricultural metabolism.