Abstract Climate change has increasingly adverse effects on global crop yields through the occurrence of heat waves, water stress, and other weather-related extremes. Besides losses of average yields, a decrease in yield stability—i.e. an increase in variability of yields from year to year—poses economic risks and threatens food security. Here we investigate a number of climate indices related to adverse weather events during the flowering of wheat, maize and rapeseed, in the current cultivation areas as well as the main European producer countries. In 52 projections from regional climate models, we identify robust increases in the interannual variability of temperature, precipitation and soil moisture by ∼+20% in standard deviation in the model median. We find that winter wheat is most exposed to variability increases, whereas rapeseed flowering escapes the largest increases due to the early flowering time and the northern locations of cultivation areas, while the opposite (escape due to southern locations and late flowering) is true for maize to some extent. Considering the timing of crop development stages, we also find a robust increase in the variability of the temporal occurrence of flowering, which suggests a decreased reliability in the timing of crop stages, hampering management steps like fertilization, irrigation or harvesting. Our study raises concerns for European crop yield stability in a warmer climate and highlights the need for risk diversification strategies in agricultural adaptation.