Innovations have the potential to help us address and overcome many of the challenges that agriculture is facing today. Yet, at the same time, they have the potential to create new, sometimes even more challenging, problems, especially when they are not governed in a sustainable way. Governing agricultural innovation sustainably requires understanding of all components that influence, and are influenced by, innovation processes, interactions across societal levels, and the normative and power dynamics that come together to shape the direction and outcomes of innovation processes. Hitherto, approaches to (agricultural) innovation and transition tend to specialize on a specific societal scale or sub-aspect of innovation or transition processes. In this article we aim to bring the strengths of some of the main approaches (Multi-Level Perspective, Agricultural Innovation Systems, Responsible Innovation, Innovation Management, Theory of Planned Behaviour) and insights from environmental governance literature together into a comprehensive framework. The framework describes seven key components and their interactions: macro context, governance system, immediate context, innovative and adaptive capacity of the actors, psychosocial factors, and the innovation process itself. Based on these, we present a subset of guiding questions that can be used diagnostically or for design purposes to support the sustainable governance of agricultural innovation processes.