The availability of coherent time series of crop statistics is essential for better analyzing the past, understanding the present, and predicting future trends in yield, area, and production. Importantly, such data also underpin assessments and subsequent policy actions that can shape future food systems that are more resilient in the face of climate change and that are sustainable in terms of resource use efficiency. In the European Union (EU), there currently is no legal obligation for EU countries to provide subnational crop statistics. However, such data could improve in-season crop forecasts, climate change impacts and adaption need assessments, and evaluation of agri-environmental schemes. The dataset described in this paper includes a harmonized collection of subnational crop statistics on area, production, and yield, collected for the EU from National Statistical Institutes (NSIs) and the EUROSTAT REGIO database – subnational crop statistics voluntarily contributed by EU countries. The crops considered are wheat (including soft and durum wheat), barley (including winter and spring barley), grain maize, sunflower, and sugar beet. All data are harmonized towards the hierarchical structure of the EUROSTAT legend and the regional classification of NUTS (Nomenclature of Territorial Units for Statistics) version 2016, to provide coherent time series. A total of 344 282 records is presented here (115 974 for wheat, 122 705 for barley, 35 274 for grain maize, 34 916 for sugar beet, and 35 413 for sunflower) for a total of 961 regions in 27 EU countries. Statistics are reported from 1975 to 2020, with a median time-span range of 21 years. A flagging system details, for each data record, information on data sources, processing steps, and quality-checking results. This includes consistency checks between reported values for area, yield and production, identification of null values, missing and calculated data, information on crop legend matching, and NUTS versioning. We illustrate the value of this dataset by analyzing impacts on crops and production zone shifts in Europe due to climatic and economic factors. Recommendations and future developments of collecting subnational statistics at the EU level are briefly discussed. The dataset is accessible with European Commission Authentication Service (ECAS) login at https://doi.org/10.2905/685949ff-56de-4646-a8df-844b5bb5f835 (Ronchetti et al., 2023b).