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The objective of our analysis was to demonstrate a novel application of production risk (probability of a yield falling below a certain level) and yield stability analysis based on the totalized yield across a 'sugar beet-winter wheat-spring barley' crop rotation. We evaluated a long-term experiment spanning more than 60 years regarding the effect of mineral NPK fertilization and the additional supply of manure on the production risk, the risk development over time (trend), and the stability of biomass yields. We found that positive impacts such as reduced production risk and enhanced yield stability were the highest for the mineral N supply, were intermediate for the K supply, and were the lowest for the P supply. The full amount of the mineral nutrient fertilization, particularly in combination with an additional manure supply, resulted in lower production risk and more stabilized crop rotational yields compared to one-half the amount of nutrient supply. The mineral fertilization of NPK (at one-half and a full amount) led to a decreasing risk trend, particularly with the additional manure supply. The risk trend of the variants with P and K (but without N) or even no mineral nutrient fertilization only decreased over time with the manure supply. The lowest production risk and the best combination of high and stable yields of the crop rotation were found at full mineral NPK fertilization in addition to manure. In contrast, the highest production risk and the worst combination of the lowest and most unstable yields were obtained under a fertilization regime without N or even under nonfertilized management. The production risk and yield stability of this fertilization regime could be reduced via regular manure application carried out once per three-year rotation during the experimental period.