It will stay sunny and dry for the most part in September in the Sacred Valley, and this month is still officially dry season in the Andes. However, there will be marginally more chance of rain than in high season and it will also be slightly warmer overall: you’ll experience highs around 68° F (20° C) and lows around 41° F (5° C).
Overall, it is a great month for hiking and for camping out under the stars. Wet weather is on its way, though, from next month, so September is your last chance to make the most of the dry season's favorable conditions for outdoor activities.
Dryer weather in cloud forest and rainforest too means you can follow up your Machu Picchu visit with a trip to the jungle, a day's journey from Cusco.
Crowds & Costs
There are better prices on hotels and activities than the high season of June through August offered. Despite the drop in costs, this is still a common month to visit Machu Picchu and it is wise even now to book popular hotels close to Machu Picchu, the Inca Trail and trains from Cusco to Aguas Calientes several months in advance.
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Where to Go
You will have certain parts of the countryside in the Sacred Valley almost to yourself in September, so try visiting some of them. There are other Inca ruins around Cusco such as Q'enqo or Sacsayhuaman, close to the city, or the impressive Moray, Pisac or Ollantaytambo sites further into the Sacred Valley. And there are other treks: Salkantay or Lares, for example, both of which incorporate multiday hikes to arrive at Machu Picchu.
What to Do
Trekking, the main activity in the Sacred Valley, remains very popular this month. Alternative ideas to the Inca Trail include a 5-day Salkantay trek, which scales a stunning mountain pass and visits Inca ruins such as those at Llactapata before arriving at Machu Picchu.
September is a great month for birders hereabouts. In the Andes, it is mating season for one of the country's most charismatic and colorful birds, the Andean cock-of-the-rock: these bright orange birds are at their most spectacular during this time, and often visible on the Inca Trail. September is also when northern migrant species of bird begin to descend on Peru.
As this is one of the best all-round months for both trekking and jungle visits, you could try combining both on your trip to Peru: this 12-day tour to the Sacred Valley and Amazon jungle for example.
It is a quieter month for festivals in the Sacred Valley following an almost continual three months of celebrations, with one important exception.
Señor de Huanca: On September 14, pilgrims from all over Peru, Bolivia and some other locations in South America come to Cusco to embark on the 6-hour pilgrimage by foot to the beautiful chapel of Santuario Señor de Huanca close to the town of San Salvador. The story of the pilgrimage dates from the 17th century when Christ allegedly appeared in a cave to one Diego Quispe whose detailed account of the incident inspired a well-known painter to reproduce the picture on a rock. The faithful come in search of all manner of cures for various ailments.