The case for solving the environmental crisis through a bioeconomic transition is gaining momentum. However, aims and content of such a transition remain unclear, as this could target an economic sector, the analysis of economic activities, or society as a whole, especially in its relationship to the biosphere. This last possible object of transition – society – is where values, models and goals come into conflict. This study examines this controversy through the lens of the ‘bioeconomics vs bioeconomy’ debate, in which proponents of bioeconomics have raised an arsenal of critiques against what they consider the simplistic promises of public and private promoters of the bioeconomy. We discuss these critiques, which are mainly macro in scale and/or narrative-centred, and argue for a complementary research effort that supports transition initiatives. This research could take place on three fronts: better understanding bioeconomic systems, evaluating bioeconomic transitions, and identifying how to implement these transitions.