Agriculture intensification is one of the most impacting drivers of European biodiversity decline. The Natura 2000 (N2000) network constitutes a key tool for conservation of species and natural habitats in Europe. Its action to counteract negative impacts of agriculture is mainly based on implementation of Agri-environment schemes (AES) in the N2000 sites. As economical resources are usually limited, spatial targeting is essential for such conservation policy. Here we evaluated whether AES distribution was in spatial coordination with species and habitat conservation states, and agriculture-driven pressures in the French N2000 network. Using the Pressure-State-Response framework, we tested the hypothesis that AES were mainly implemented in sites mostly exposed to pressures, having higher representativeness of species and habitats and higher degradation levels. We combined different sources of information (i.e., standard data forms of the N2000 policy, data collected by the observatory of rural development and national geographical information) to produce pressure, state and response spatial indicators. We declined the analysis per category of pressures related to agricultural activities and considered species and habitat vulnerability to each pressure category. We found limited spatial coordination between AES, pressure and state variables: only 37 % of the fitted models were significant. Significant relationships between AES implementation and agricultural intensification pressure were mostly negative. Considering all indicators, our hypotheses were disproven for more than half of the significant relationships. The results revealed a spatial mismatch between AES distribution and the ecological needs within the N2000 network, as more resources were devoted to sites less exposed to pressure. Our results raise the need of a more strategic approach for the N2000 policy. Indeed, the state of biodiversity conservation and the level of human pressures should be automatically considered a-priori of any implementation of management measures to effectively focus the efforts on the causes of current biodiversity crisis. •We assess agri-environmental schemes (AES) targeting in French Natura 2000 network.•AES distributions compared to agricultural pressures and biodiversity variables.•AES financial expenses and cover poorly target pressures and biodiversity.•More AES are implemented in Natura 2000 sites showing less agricultural pressures.•Better efficiency of N2000 policy needs strategic approaches for AES implementation.