The impacts of agricultural, environmental and climate change policies in Europe are investigated using the CAPRI (Common Agricultural Policy Regionalised Impact) model. Although the model runs at a regional level, primarily NUTS2, the underlying data have been spatially disaggregated to finer scale units called ‘Farm Structure Units’. In this study we present these spatially disaggregated layers of agri-environmental variables for a time series from 2000 to 2018. This harmonized and spatially consistent data set includes crop types (area, yield), livestock types (totals and densities) and various parameters associated with nitrogen application and losses. These data can be used to calculate nitrogen budgets as well as providing inputs to biogeochemical or land management models.