One of the major challenges in agriculture is how climate change influences crop production, for different environmental (soil type, topography, groundwater depth, etc.) and agronomic management conditions. Through systems modelling, this study aims to quantify the impact of future climate on yield risk of winter wheat for two common soil types of Eastern Denmark. The agro-ecosystem model DAISY was used to simulate arable, conventional cropping systems (CSs) and the study focused on the three main management factors: cropping sequence, usage of catch crops and cereal straw management. For the case region of Eastern Denmark, the future yield risk of wheat does not necessarily increase under climate change mainly due to lower water stress in the projections; rather, it depends on appropriate management and each CS design. Major management factors affecting the yield risk of wheat were N supply and the amount of organic material added during rotations. If a CS is characterized by straw removal and no catch crop within the rotation, an increased wheat yield risk must be expected in the future. In contrast, more favourable CSs, including catch crops and straw incorporation, maintain their capacity and result in a decreasing yield risk over time. Higher soil organic matter content, higher net nitrogen mineralization rate and higher soil organic nitrogen content were the main underlying causes for these positive effects. Furthermore, the simulation results showed better N recycling and reduced nitrate leaching for the more favourable CSs, which provide benefits for environment-friendly and sustainable crop production.