In recent years, evidence of recent climate change has been identified in South America, affecting agricultural production negatively. In response to this, our study employs a crop modelling approach to estimate the effects of recent climate change on maize yield in four provinces of Ecuador. One of them belongs to a semi-arid area. The trend analysis of maximum temperature, minimum temperature, precipitation, wind speed, and solar radiation was done for 36 years (from 1984 to 2019) using the Mann–Kendall test. Furthermore, we simulated (using the LINTUL5 model) the counterfactual maize yield under current crop management in the same time-span. During the crop growing period, results show an increasing trend in the temperature in all the four studied provinces. Los Rios and Manabi showed a decreasing trend in radiation, whereas the semi-arid Loja depicted a decreasing precipitation trend. Regarding the effects of climate change on maize yield, the semi-arid province Loja showed a more significant negative impact, followed by Manabi. The yield losses were roughly 40 kg ha−1 and 10 kg ha−1 per year, respectively, when 250 kg N ha−1 is applied. The simulation results showed no effect in Guayas and Los Rios. The length of the crop growing period was significantly different in the period before and after 2002 in all provinces. In conclusion, the recent climate change impact on maize yield differs spatially and is more significant in the semi-arid regions.