September in Puerto Ayora is the windiest, the cloudiest, and the coldest month of the year. In September, the weather in Puerto Ayora is typically warm. Average daily high temperature in September is about 22 degrees above zero. On average, Puerto Ayora has 20 partly cloudy, 5 sunny, and 5 cloudy days in September. September as well as June, July, August, and October is considered the most comfortable time to visit Puerto Ayora.