While the quantity of sustainability governance initiatives and systems has increased dramatically, crises persist over whether specific governance systems can be trusted as legitimate regulators of the sustainability of economic activities. This paper focuses on conceptual tools to improve our understanding of these crises as well as the facilitating factors and barriers for sustainability governance to play a role in transitioning to profoundly more sustainable societies than those that currently exist. Bioenergy is used throughout the paper as an example to aid contextually in understanding the theoretical and abstract arguments. We first define eight premises upon which our argumentation is developed. We then define sustainability, sustainability transition, legitimacy, and trust as a premise for obtaining effectiveness in communication and minimising risks associated with misunderstanding key terms. We proceed to examine the literature on “good governance” in order to reflect upon what defines "good sustainability governance" and what makes governance systems successful in achieving their goals. We propose input, output, and throughput legitimacy as three principles constituting “good” sustainability governance and propose associated open-ended criteria as a basis for developing operational standards for assessing the quality of a sustainability governance system or complex. As sustainability governance systems must develop to remain relevant, we also suggest an adaptive governance model, where continuous re-evaluation of the sustainability governance system design supports the system in remaining “good” in conditions that are complex and dynamic. Finally, we pull from the literature in a broad range of sciences to propose a conceptual “governance research framework” that aims to facilitate an integrated understanding of how the design of sustainability governance systems influences the legitimacy and trust granted to them by relevant actors. The framework is intended to enhance the adaptive features of sustainability governance systems so as to allow the identification of the causes of existing and emerging sustainability governance crises and finding solutions to them. Knowledge generated from its use may form a basis for providing policy recommendations on how to practically solve complex legitimacy and trust crises related to sustainability governance.