A recently implemented research and development (R&D) programme in New Zealand is attempting to implement co-innovation principles throughout the country’s agricultural sector. It is based on an agricultural innovation systems (AIS) approach, using five innovation platforms (IPs) based in the leading industries, plus a national-level IP. This paper presents and analyses the emerging challenges of operationalizing transdisciplinary research connected to co-innovation in the context of the programme. The main challenges relate to managing the complexity of a multi-stakeholder network, aligning the formal procedures for research funding and IPs with a co-innovation approach that requires flexibility, and changing participants’ framing of innovation from linear to interactive models. Our conclusion is that ‘learning by doing’ is essential in operationalizing coinnovation. Its practical implications still need to be translated into institutional changes in the national R&D structures so that policies, instruments and incentives enable co-innovation. It is envisaged that the higher-level innovation platform will drive these changes.