Introduction: Climate change (CC) and the increased occurrence of extreme climatic events pose a serious threat to crop yields and their stability worldwide. This study analyzed the CC mitigation potential of an alley cropping system on crop physiological stresses and growth as compared to a monoculture system. Materials and Methods: Growth of winter durum wheat, cultivated alone (agriculture) and in combination with hybrid walnut (agroforestry), was simulated with the Hi-sAFe agroforestry model, as driven by business-as-usual Intergovernmental Panel on Climate Change (IPCC) projections, split into three scenarios, representing Past (1951–1990), Present (1991–2030), and Future (2031–2070) climatic conditions. Crop growth and the occurrence of thermal, nitrogen, and water stresses were analyzed. Results: Cold-related stresses were modest in Past and almost disappeared over time. Heat, drought, and nitrogen stresses increased about twofold from Past to Future, but were reduced by 20–35% in agroforestry, already with medium-sized trees (diameter at breast height (DBH) of about 10–15 cm). Crop yields in agriculture increased from Past to the end of Present and then remained stable. This moderately decreased with tree age in agroforestry (especially in Future). Discussion: The impact of CC on the crop was buffered in agroforestry, especially for the most extreme climatic events. The mitigation of crop microclimate and the increased stability of crop yields highlight the potential of agroforestry as a CC adaptation strategy.