Given the growing interest in drought impacts on crops, this work studied the impact of agricultural drought on wheat and barley during the period 2001–2020. The study was carried out in the Spanish regions of Castilla y León and Castilla–La Mancha, with approximate areas of 94,000 km2 and 79,000 km2, respectively, and in the German regions of Nordrhein-Westfalen, Niedersachsen and Bayern, with approximate areas of 34,000 km2, 48,000 km2 and 71,000 km2, respectively. These are the main cereal-growing regions of Spain and Germany. Soil moisture (SM) in the root zone was extracted from the LISFLOOD model database, and SM anomalies were used as the agricultural drought index. Gross primary productivity (GPP) and leaf area index (LAI) variables were obtained from the Moderate Resolution Imaging Spectroradiometer (MODIS), and the month in which SM is most influential on these crop state variables was identified. Crop yields in Spain and Germany were obtained from the Spanish Ministry of Agriculture, Fisheries and Food and the German Federal Statistical Office, respectively. Agricultural drought years and their impact on cereal yields were determined on a regional scale using three approaches based on the critical month with different time periods. These approaches were the use of the critical month and the two (before or after) and the three months (before and after) around the critical month. Two different analyses were used to identify the critical month, depending on the different environmental conditions in each country. These two approaches consisted of a monthly correlation analysis between SM anomalies and cereal yield in Spain and a monthly trend analysis of SM anomalies in Germany. The results showed a dependence of crop variables on SM in spring months in both countries and in summer months in Germany. Differences were found depending on the environmental conditions. A considerable reduction in cereal yields was obtained in Spain which exceeded 30%. Similarly, a worrying sign was observed in Germany, with a positive agricultural drought trend and a yield reduction of almost 5% in cereal crops. In view of future forecasts of the negative impact of climate change on global food production, this study provides valuable information for water and agricultural management under climate change scenarios. Both in regions that are already threatened and in those that until recently were not affected, it is necessary to study adaptation measures to avoid aggravating the impact of agricultural drought on crops, which could improve water productivity and future food security.