This paper examines the role played by biodiversity goals in the design of agricultural policies. A bio-economic model is developed with a dynamic and multi-scale perspective. It combines biodiversity dynamics, farming land-uses selected at the micro level and public policies at the macro level based on financial incentives for land-uses. The public decision-maker identifies optimal subsidies or taxes with respect to both biodiversity and budgetary constraints. These optimal policies are then analysed through their private, public and social costs. The model is calibrated and applied to metropolitan France at the small agricultural region scale, using common birds as biodiversity metrics. First results relying on optimality curves and private costs stress the bio-economic trade-off between biodiversity and economic scores. In contrast, the analysis of public costs suggests that accounting for biodiversity can generate a second benefit in terms of public budget. Social costs defined as the sum of private and public costs also show possible bio-economic synergies.