Climate change is expected to affect the agricultural sector in ways that are often unclear to predict. If in the short- and medium-terms farmers may adapt to climate change by adjusting their agricultural practices, in the long-term, these adjustments may become insufficient, forcing farmers to change their farming systems. The extent and direction in which these farming system transitions will occur is still a subject that is underexplored in the literature. We propose a new framework to explore the effect of climate change on the choice of farming system while controlling the effect of other drivers that are also known to influence the farming system choice. Using a spatially explicit farming system choice model developed by a previous study in an extensive agricultural region of southern Portugal, we applied a space-for-time approach to simulate the effect of climate change on the future dynamics of the farming systems in the study area. The results suggest that climate change will force many farmers to change the farming system in a foreseeable future. The extent of the projected changes in farming systems is likely to trigger significant social, economic, and environmental impacts, which should require early attention from policy makers.