Intensification of farming practices is still a major driver of biodiversity loss in Europe, despite the implementation of policies that aim to reverse this trend. A conceptual framework called MIRABEL was previously developed that enabled a qualitative and expert-based assessment of the impact of agricultural intensification on ecologically valuable habitats. We present a quantitative update of the previous assessment that uses newly available pan-European spatially explicit data on pressures and habitats at risk. This quantitative assessment shows that the number of calcareous grasslands potentially at risk of eutrophication and overgrazing is rapidly increasing in Europe. Decreases in nitrogen surpluses and stocking densities that occurred between 1990 and 2000 have rarely led to values that were below the ecological thresholds. At the same time, a substantial proportion of calcareous grassland that has so far experienced low values for indicators of farming intensification has faced increases between 1990 and 2000 and could well become at high risk from farming intensification in the near future. As such, this assessment is an early warning signal, especially for habitats located in areas that have traditionally been farmed extensively. When comparing the outcome of this assessment with the previous qualitative MIRABEL assessment, it appears that if pan-European data are useful to assess the intensity of the pressures, more work is needed to identify regional variations in the response of biodiversity to such pressures. This is where a qualitative approach based on regional expertise should be used to complement data-driven assessments.