Evaluating the effectiveness of conservation funding is crucial for correct allocation of limited resources. Here we used bird monitoring data to assess the effects of long-term conservation investment in a Natura 2000 (N2000) bird protection area (PA), which during two decades benefited from protection regulations, conservation projects, and agri-environment schemes. Variation between 1995–1997 and 2010–2012 in richness and abundance of flagship (Otis tarda, Tetrax tetrax, and Falco naumanni) and specialized fallow field species were more favorable (i.e., increased more or declined less) inside the PA than in a nearby control area. However, the reverse was found for total bird species, farmland, ground-nesting and steppe species, species associated to ploughed fields, and species of European conservation concern. Enhancing the effectiveness of conservation investment in N2000 farmland may require a greater focus on the wider biodiversity alongside that currently devoted to flagship species, as well as improved matching between conservation and agricultural policies.