For several decades, significant changes in farmland biodiversity have been reported in Europe. Agriculture is a major driver of these modifications. Taking into account these environmental impacts, agriculture nowadays aims at a more sustainable way of producing which would reconcile its economic and ecological functions. The objective of this paper is to give insights into the impact of public policies on both conservation of biodiversity and farming production. We develop a macro-regional model combining community dynamics of 34 bird species impacted by agricultural land-uses and an economic decision model. The ecological dynamic model is calibrated with the STOC (French Breeding Bird Survey) and AGRESTE (French land-uses) databases while the economic model relies on the gross margins of the FADN (Farm Accountancy Data Network). We investigate the scenario based on subsidies and taxes. We show that simple economic instruments could be used to establish scenarios promoting economic performances and bird populations. It is pointed out how the sustainability of the policies is sensitive to the ecological and economic indicators used by the planner. The bio-economical analysis shows several solutions for the ecology-economy trade-off. These results suggest that many possibilities are available to develop multi-functional sustainable agriculture.