In September, the weather in San Miguel de Allende is typically warm. Average daily high temperature in September is about 25 degrees above zero. On average, San Miguel de Allende has 13 rainy, 9 partly cloudy, 6 sunny, and 2 cloudy days in September. The rains are usually heavy. September as well as June, July, and August is considered the most uncomfortable time to visit San Miguel de Allende.