Limited information is available on the management and delivery of national-scale biodiversity projects. Even less information is available on such projects operating in agricultural matrices, particularly how they address the expectations of multiple stakeholders from paddock to farm, regional and national scales. This paper describes the approach taken to implement and deliver the Biodiversity in Grain & Graze project, which was national in focus, regional in operation and local in delivery. The project was instigated by four research and development corporation partners who were keen to connect the interests of mixed-farming producers to the environmental goals of nine collaborating regions across Australia. One aim of the project was to engage producers in participatory research on the biodiversity values of mixed-farming systems. This aim could not have been met without considerable effort building regional capacity in biodiversity research and developing a national network of researchers, regional extension staff and stakeholders. This national network was engaged primarily through program and project workshops, regular electronic communications and site visits. Levels of engagement were high, resulting in a sense of ownership by all stakeholders, counteracting to some degree the ill feeling associated with the late inclusion of the biodiversity project to regional activities. Issues relating to goal confusion were evident throughout the whole project, despite a concerted effort by the project team to address such tensions. Previous studies have indicated, and we concur, that biodiversity components need to be built into programs like Grain & Graze at the beginning, and need to be developed in consultation with farmers, regional agencies and research organisations to ensure that expectations are shared and the project is fully supported.