This paper builds on the literature on mission-oriented innovation policy, governance, transition studies and innovation systems, and develops a structural-functional approach to formatively evaluate mission governance from a Mission-oriented Innovation Systems (MIS) perspective. Central to this MIS approach is the mission arena, a governance structure where actors formulate and govern the mission, by mobilizing and directing other, preexisting system components. Their goal is to meet the mission by developing and diffusing innovative mission solutions and destabilizing harmful practices. The MIS approach involves a problem-solutions diagnosis and an analysis of structural, functional, and systemic barriers. To provide formative mission governance recommendations, the systemic barriers are then contrasted with the mission arena’s governance tasks. To illustrate the value of the MIS approach, we use a case study of the Dutch mission for sustainable maritime shipping. This case study illustrates a mission arena striving to increase coherence amongst different innovation system structures in semblance of a MIS. The mission arena configuration of actors shaped the mission formulation and negotiated governance actions. Dominant industry networks negotiated green growth as problem direction and non-committal governance actions, which are likely ineffective for inherently transformative sustainability missions. The paper concludes by identifying directions for further developing the MIS approach and the mission arena concept.