ABSTRACT Introduction and Aim The mapping and monitoring of ecosystem size and extent is critical for assessing changes in the environment. Mapping approaches typically include the use of expert‐based assessments and remotely sensed products. In this work, we present a new annual high‐resolution time series dataset of ecosystem units for Europe that integrates a range of different data sources. In total, 411 different distinct ecosystem units were identified in the EU27+, with large patches of woodland and forest in cold climates and temperate climate croplands on plain terrain as the two most commonly occurring types in 2000. Over the 18 year period, only 56 ecosystems remained stable, with area increases in 192 ecosystem types but losses in area in 163 of them. Furthermore, we highlight gaps in representation for 16.8% of all ecosystem units in the current protected area network. Main Variables Included Corine Land cover time series, Landforms, climate, patch size. Time Coverage 2000 to 2018. Spatial Coverage 100 m spatial resolution at pan‐European extent. Taxa Ecosystem assessment. Applications The dataset is consistent with previous EU ecosystem accounting assessments, while providing additional detail on climate, landform and fragmentation. It can serve as a data source, for example, for ecosystem accounting, conservation planning, or species distribution modelling.