Extreme weather increases the risk of large-scale crop failure. The mechanisms involved are complex and intertwined, hence undermining the identification of simple adaptation levers to help improve the resilience of agricultural production. Based on more than 82 000 yield data reported at the regional level in 17 European countries, we assess how climate affected the yields of nine crop species. Using machine learning models, we analyzed historical yield data since 1901 and then focus on 2018, which has experienced a multiplicity and a diversity of atypical extreme climatic conditions. Machine learning models explain up to 65% of historical yield anomalies. We find that both extremes in temperature and precipitation are associated with negative yield anomalies, but with varying impacts in different parts of Europe. In 2018, Northern and Eastern Europe experienced multiple and simultaneous crop failures—among the highest observed in recent decades. These yield losses were associated with extremely low rainfalls in combination with high temperatures between March and August 2018. However, the higher than usual yields recorded in Southern Europe—caused by favourable spring rainfall conditions—nearly offset the large decrease in Northern European crop production. Our results outline the importance of considering single and compound climate extremes to analyse the causes of yield losses in Europe. We found no clear upward or downward trend in the frequency of extreme yield losses for any of the considered crops between 1990 and 2018.