Agricultural management is a major driver of changes in floral and faunal species richness of anthropogenic landscapes. Counteracting the negative impact of industrialized agriculture by providing subsidies to farmers for environmentally friendly agricultural practices, agri-environmental schemes (AES) are the most important policy instruments to protect European biodiversity in agricultural landscapes. However, as they are rarely cost-effective, there is an urgent need for evaluation and improvement. To assess the environmental effects of the Austrian AES, we mapped landscapes and vascular plants in 1998 and 2003 and birds in 2003. The sampling areas were located in the three most important types of Austrian agricultural landscape, i.e., grassland in alpine valleys and basins, mixed agriculture in mountain areas, and eastern arable land. We investigated the agri-environmental measures (AEMs) in a parcel-wise manner and analyzed their effects on landscape values and biodiversity. Reduction of agrochemicals showed positive effects on biodiversity of vascular plants in grassland and birds in arable land. Targeted measures that directly address threatened species were most effective, but had much less coverage. Contradicting developments became apparent for landscape structure and ecological infrastructures, but effects of the AES were generally larger in simple than in complex landscapes. We conclude that AEMs are currently not targeted enough to effectively halt biodiversity losses, and recommend better regionalization by offering landscape-context specific measures, stronger focus on maintenance and improvement of landscape diversity, avoidance of counterproductive development, and improvement of the coverage of specific conservation measures.