Abstract:The purpose of this paper is to identify, analyse and discuss the key governance challenges for the emerging Knowledge-Based Bio-Economy (KBBE) in Europe focusing on bioenergy, particularly biofuels for transport and the biorefinery concept. This paper is based on a literature review, discussions with European researchers and practitioners, and questionnaires of bioenergy industry associations. The growing bio-economy and bioenergy in Europe face a host of socio-technical issues that comprise a mix of technological, economic, social, political, environmental, regulatory and cultural aspects. More specifically, this research work highlights three key governance challenges of increasing relevance for the bio-economy, including: the important role of public-private networks; city-regions as drivers for the KBBE, especially through climate governance; and consumer-citizens and NGOs as key players in the development of the bio-economy.