Abstract Literature on mission-specific innovation systems (MIS) highlights the crucial role of directionality when achieving sustainability transitions, while diversity literature emphasizes the need to keep diverse directions open. Like directionality, diversity is created by innovation system actors to tackle the complex and uncertain nature of transitions. While these two literature strands are presented largely independent of one another, both are deemed necessary to achieve sociotechnical transitions. We thus aim to uncover how diversity and directionality unfold in parallel in a MIS. We conduct a qualitative single-case study of the Wageningen alternative protein ecosystem to provide insights into the types of sociotechnological trajectories actors pursue and how different selection environments shape the development of each solution. We observe a mission exhibiting a clear direction toward (meat) substitutes. Underlying this mission, diversity is visible. We propose that the interplay between diversity and directionality in a MIS can be best understood by distinguishing two different sociotechnical “levels” in which they play out: the levels of transition paths (“first-order” directionality) and search directions (“second-order” directionality). We therefore call for a more nuanced understanding of the role of diversity and directionality in transitions.