Agricultural innovation systems has become a popular approach to understand and facilitate agricultural innovation. However, there is often no explicit reflection on the role of agricultural innovation systems in food systems transformation and how they relate to transformative concepts and visions (e.g. agroecology, digital agriculture, Agriculture 4.0, AgTech and FoodTech, vertical agriculture, protein transitions). To support such reflection we elaborate on the importance of a mission-oriented perspective on agricultural innovation systems. We review pertinent literature from innovation, transition and policy sciences, and argue that a mission-oriented agricultural innovation systems (MAIS) approach can help understand how agricultural innovation systems at different geographical scales develop to enable food systems transformation, in terms of forces, catalysts, and barriers in transformative food systems change. Focus points can be in the mapping of missions and sub-missions of MAIS within and across countries, or understanding the drivers, networks, governance, theories of change, evolution and impacts of MAIS. Future work is needed on further conceptual and empirical development of MAIS and its connections with existing food systems transformation frameworks. Also, we argue that agricultural systems scholars and practitioners need to reflect on how the technologies and concepts they work on relate to MAIS, how these represent a particular directionality in innovation, and whether these also may support exnovation.