Livestock farms are an important source of ammonia emissions, which threaten vulnerable habitats and species in nearby natural areas through a process of atmospheric nitrogen deposition. An integrated and spatially- explicit mixed integer programming model was applied to all livestock facilities in Flanders (Belgium), to evaluate the current Flemish policies aimed at limiting ammonia deposition in Natura 2000 sites. The simula- tions indicate that a substantial reduction in deposition is achievable with a similar cost to the currently applied policy in Flanders. Furthermore, the model allows identification of the most suitable stable type and emission abatement measures for any stable in Flanders. Such a spatially-explicit optimization approach applied to in- dividual emission sources might assist policymakers in improving spatially-differentiated policies.