The fact that the expansion and intensification of agriculture has been the major driver of past biodiversity loss and ecosystem degradation globally is beyond dispute. It is highly likely that these trends will continue through the 21st century, unless action is taken to design effective management strategies for biodiversity in agricultural landscapes. To do this, we first need to recognize that some biodiversity is retained in farmland, and that it is the degree of biodiversity retention that we need to understand and effectively manage. We need to understand which biodiversity components are retained as a natural ecosystem is converted to agriculture and why; how community dynamics affect biodiversity retention; and how we can effectively manage biodiversity retention. These questions are being addressed, but much remains to be done; and we have to accept that progress will be contentious. Challenging as these questions are, conservationists cannot address them in isolation. Multifunctional ecosystem science and policy linked to human well-being is the ultimate goal. While the goal seems distant and daunting, integration between relevant research disciplines is happening, research funding is beginning to recognize the need for better integration and policy has to respond. Conservation science has a key role to play and must be ready to meet this challenge.