The business of agricultural research, development and extension (RD&E) has undergone considerable change in Australia since the late 1980s, moving from a domain largely dominated by government departments to a situation of multiple actors, and where rural industries now directly contribute funds towards RD&E efforts. However, the transition has not been without impacts on the overall agricultural RD&E agri-food capacity of the nation, and there are now indications of reduced capacity and slowing productivity gains in certain sectors. If not addressed, there is the risk that the future resilience of industries could be threatened, affecting parts of the Australian economy and compromising Australian contributions to global food supply on export markets and a slowing of agricultural innovation. There are also comparable divestment trends and the loss of capacity and risks to future resilience of agricultural systems in other developed nations. Importantly, research and extension are discussed as interdependent partner disciplines, and that the separation of the two has deleterious effects on capacity and resilience building. The authors investigate, through six case study institutions, organisational innovations that may provide direction towards the future restructuring of agricultural RD&E effort in Australia. These insights have application to both the Australian and the international reader, warning about the consequences of reduced investment in agricultural RD&E, and learning about how research and extension can transition from traditional public sector models to systems that have greater flexibility and, importantly, ownership by the industries themselves.