The bioeconomy is a worldwide used strategy to cope with ecological, social, and economic sustainability challenges. However, we analyze current bioeconomy strategies and trends to point out potential sustainability conflicts and transition challenges. Our analysis shows that the bioeconomy is not sustainable per se, as mere input substitution may entail welfare losses. Instead, it requires further debates and actions to avoid exacerbation of ecological and social strains. Sustainability has to be the key concept behind the bioeconomy and predominantly requires (1) sustainability of the resource base and (2) sustainability of processes and products, especially by (3) circular processes of material fluxes, not least to gain consumer acceptance for bio-based products. Otherwise, the bioeconomy would only entail the substitution of fossil resources for bio-based resources potentially lacking the generation of additional societal and ecological benefits and contribution to climate mitigation. As markets alone will not suffice to fulfil this path transition towards a sustainable bioeconomy, we argue that innovative governance is necessary to reduce competitive drawbacks compared to fossil resources (enabling function) and to secure ecological, social, and economic sustainability requirements (limiting function).