The impact of climate change on cotton and maize was estimated on the basis of three IPCC Emission Scenarios (A1B, A2, B2) for seven main agronomic areas during three periods, 1961–1990, 2021–2050 and 2071–2100. All climate models were assessed for their ability to identify the yield differences through the standardized discriminant function coefficients. Discriminant analysis was performed for each period. For cotton, using the A1B scenario, areas of Western Greece exhibited the most favourable results in terms of yield increase, compared to other regions, ranging up to the maximum value of +24%. This tendency became more pronounced towards the end of the century reaching an increase of +31%. In the A2 scenario, all the areas had a positive impact on their yield change rising up to 30% in areas of central Greece. A positive change for all regions was observed for scenario B2 ranging from +10% to +25%. In maize, the scenario A1B produced small changes in yields, not exceeding 5%. For A2 scenario, yield change varied from −5.7% to +3.6%. Scenario B2 gave more optimistic estimates of yield changes towards the end of the century, in some cases exceeding 5%.