In the last decades, problems related to environmental protection have become more and more important, involving a growing number of economic and social actors. The new role played by agriculture in this context requires not only innovations concerning policy instruments, but also an evolution of tools, such as those for environmental accounting and assessment, able to support the analysis of choices in a complex economic and technological context, characterised by a number of heterogeneous objectives. This paper illustrates a model (AGRI-ECO-AUDIT) set up with the aim of supporting decision making concerning the application of Reg. (EEC) 2078/92 in Emilia-Romagna (Italy). The aim is to verify the possible contribution of environmental accounting to environmental protection and improvement in agriculture and to identify policy strategies for the exploitation of such potentialities in order to improve agricultural and agri-environmental policies. The case study discussed here shows that the use of accounting tools for measuring and evaluating the multidimensional impact of policies and farming practices on the environment can improve considerably the information available for the decision maker, allowing a higher effectiveness of agri-environmental policy measures.