The impact of a changing climate on crop and tree growth remains complex and uncertain. Whilst some areas may benefit from longer growing seasons and increased CO2 levels, others face threats from more frequent extreme weather events. Models can play a pivotal role in predicting future agricultural and forestry scenarios as they can guide decision-making by investigating the interactions of crops, trees, and the environment. This study used the biophysical EcoYield-SAFE agroforestry model to account for the atmospheric CO2 fertilization and calibrated the model using existing field measurements and weather data from 1989 to 2021 in a case study in Northern Ireland. The study then looked at two future climate scenarios based on the representative concentration pathways (RCP 4.5 and RCP 8.5) for 2020–2060 and 2060–2100. The predicted net impacts of future climate scenarios on grass and arable yields and tree growth were positive with increasing CO2 fertilization, which more than offset a generally negative effect of increased temperature and drought stress. The predicted land equivalent ratio remained relatively constant for the baseline and future climate scenarios for silvopastoral and silvoarable agroforestry. Greater losses of soil organic carbon were predicted under arable (1.02–1.18 t C ha−1 yr−1) than grassland (0.43–0.55 t C ha−1 yr−1) systems, with relatively small differences between the baseline and climate scenarios. However, the predicted loss of soil organic carbon was reduced in the long-term by planting trees. The model was also used to examine the effect of different tree densities on the trade-offs between timber volume and understory crop yields. To our best knowledge this is the first study that has calibrated and validated a model that accounts for the effect of CO2 fertilization and determined the effect of future climate scenarios on arable, grassland, woodland, silvopastoral, and silvoarable systems at the same site in Europe.