Agricultural research organisations play a critical role in the agri-food system; not only through the provision of research and technologies, but also by brokering relationships with stakeholders throughout the research process to create impact. Yet over the past decade, as the focus has shifted towards such multi-actor innovation processes, the role and legitimacy of the agricultural research organisations world-wide has been challenged. Occupying an intermediary position in agricultural innovation systems means that agricultural research institute legitimacy is constantly under pressure from the rural community, academics, policy makers, industry, and general society as the institute attempts to be all things to all people. Here we present the outcomes of an organisational change programme within an applied agricultural research organisation, in response to a government-led agenda to increase impact for research users. By using institutional theory of hybrid organisation legitimacy, we shed light on the multiple institutional logics that co-exist within an agricultural research institute, and how these align with the external institutional environment. We show that with the introduction of a new multi-actor innovation logic, attempts were made to legitimise, externally and internally, knowledge co-production. Yet agricultural research organisations, and those who work within them, need dedicated time for learning and reflecting on the values, beliefs, and practices of the different actors in the innovation system, otherwise they only selectively adopt practices that maintain existing institutional logics. The main theoretical implications show how that change towards an impact culture is influenced by the existing logics, and how organisational legitimacy provides a framing for understanding the success (or otherwise) of introducing new modes of innovation in hybrid research organisations. Practically, space and resourcing are needed to experiment with new logics and deliberate strategies are required to increase the repertoire of research roles while maintaining internal and external legitimacy. The practical implications demonstrate the barriers and opportunities of re-orientating hybrid agricultural research institutes, agricultural innovation systems, and the roles of the researchers that work in them, to deliver to the complex societal challenges facing the agri-food sector.