The anticipated increases in environmental variability associated with climate change may lead to enhanced abiotic plant stresses (e.g., heat stress, drought stress, etc.) resulting in greater inter-annual yield fluctuations and higher crop production risk. While there has been increasing attention to adaptation measures, there is little evidence available on how to change agronomic management strategies to maintain stable yields in winter rye production systems in Poland. This study uses rye yields from the unique Skierniewice Long-term experiment (Poland) to examine for the first-time the long-term effects of different nutrient regimes on crop yield stability from 1966 to 2015. Yields from six combinations of mineral fertilizers and lime (CaNPK, NPK, CaPK, CaNK, CaNP, Ca), with and without additional manure, were used to estimate the temporal yield variability of winter rye. A novel statistical approach based on a mixed model approach with REML (restricted maximum likelihood) stability parameter estimation was used. The results showed that the use of additional manure in ‘sub-optimal’ mineral fertilizer treatments, such as Ca and CaPK (without mineral N), reduced the temporal yield variability of rye. In contrast, additional organic input led to more variable rye yields in already ‘optimal’ treatments including mineral N (CaNPK and NPK), compared to those with no additional manure. Winter rye given CaNPK and NPK, without additional organic manure demonstrated high yield and low temporal yield variability. In contrast, yields of treatments with no mineral N (Ca and CaPK) and no additional manure supply were low and unstable. In addition, it was found that increasing soil organic carbon resulted in larger, more stable yields. These findings highlight the importance of ensuring rye crops receive sufficient fertilizer to maintain crop production levels and yield stability, especially in dry years. They also demonstrate the importance of avoiding the excessive use of organic manures when fertilizer inputs are sufficient to meet crop demand. Overall, the study provides novel insights about how to maintain grain yields and minimize temporal yield variation of rye in arable cropping systems, which will become increasingly important in a changing climate in Poland and in other temperate climate areas. This study also highlights the importance of soil organic carbon for improving the climate resilience of winter rye, while simultaneously meeting the demand for more sustainable management of the soil.