In the World Heritage Côa region, in northern Portugal, agriculture has crucial economic, social and cultural importance. Vineyards and olive groves are part of the economic base of this region, contributing to the regional commercial budget and the livelihood of its residents. Climate change is expected to have significant impacts on these crops, where climatic conditions are already very warm and dry, posing a key threat to the olive oil and winemaking sectors. The present study analyzes the impact of climate change on the potential yield of these two crops over the Côa region. For this purpose, two crop models were initialized and ran with state-of-the art spatial datasets for climate, soil, terrain, and plant data. As outputs of the crop models, potential yields of grapevines and olive trees were obtained for the recent-past (1981–2005) and for the future (2041–2070), under two climatic scenarios (RCP4.5 and RCP8.5). Results (potential yield) were then normalized, taking into account the recent-past maximum yields and divided into four classes (low, low-moderate, moderate-high, and high). For the recent-past, the results of the crop models present a high agreement with the current location of vineyards and olive groves. For the future, two different types of impacts (positive and negative) are found for the two crops. For olive trees, the results show promising future improvements in possible expansion areas within the Côa region. However, for grapevines, the results show a decrease in potential yields throughout the region, including a strong shift of producing moderate zones to low potentials. Nonetheless, these results also suggest that the negative impacts of climate change can be alleviated by the application of suitable adaptation measures, based on changing certain management practices, even in the more severe future scenario. Therefore, these measures should be carefully planned and implemented in a timely fashion by farmers.