Nitrogen deposition is one of the main environmental threats to the conservation goals in areas protected by the European Habitats Directive, a problem that is quite pronounced in the livestock-rich region of Flanders, Belgium. Livestock farms are often located close to Natura 2000 areas. Therefore, ammonia emissions from livestock housing and manure storage have a high contribution to the deposition in these nearby protected habitats. In order to control this problem, the Flemish government imposes restrictions on livestock farms with a high impact on protected habitats. Using an integrated spatially-explicit modeling approach, we were able to show that the effectiveness of this spatially-differentiated policy is rather limited in terms of the percentage of habitats in exceedance of the critical load for nitrogen. In order to obtain a good status in all habitats, emission abatement efforts should extend beyond the livestock sector. Furthermore, the policy affects some livestock subsectors more than others, while similar discrepancies are unveiled on the level of different habitat types. By means of 4 different habitat classes, the effectiveness of different policy scenarios can be easily assessed on the level of individual habitats.