We present extensions to the agent-based agricultural policy simulator (AgriPoliS) model that make it possible to simulate the consequences of agricultural policy reform on farmers’ land use decisions and concomitant impacts on landscape mosaic, biodiversity and ecosystem services in a real agricultural region. An observed population of farms is modelled as a multi-agent system where individual farm-agent behaviour and their interactions—principally competition for land—are defined through an optimization framework with land use and landscape impacts resulting as emergent properties of the system. The model is calibrated to real data on the farms and the landscape to be studied. We illustrate the utility of the model by evaluating the potential impacts of three alternative frameworks for the European Union Common Agricultural Policy (CAP) on landscape values in two marginal agricultural regions. Mosaic value was found to be sensitive to the choice of policy scheme in one of the landscapes, whereas significant trade-offs were shown to occur in terms of species richness by habitat and species composition at the landscape scale in both regions. The relationship between food production and other ecosystem services was found to be multifaceted. Thus illustrating the difficulty of achieving landscape goals in a particular region with simple or general land management rules (such as the current rules attached to CAPs direct payments). Given the scarcity of funding for conservation, the level and conditions for allocating direct payments are, potentially, of great importance for preserving landscape values in marginal agricultural regions (subject to levels of other support).