How to Plan a 2-Week Peru Itinerary Including Machu Picchu and the Amazon

Split your 2 weeks between Lima (2 days), Cusco region including Machu Picchu (6-7 days), and the Amazon (4-5 days). Book Machu Picchu permits 2-4 months ahead and choose Puerto Maldonado for easier Amazon access or Iquitos for deeper jungle experience.

  1. Book Machu Picchu permits first. Reserve your Machu Picchu entrance tickets and Huayna Picchu climb (if desired) 2-4 months in advance at machupicchu.gob.pe. You need your passport number. Choose morning slots (6am or 8am) for better weather and photos.
  2. Choose your Amazon gateway. Puerto Maldonado offers 3-4 day lodge experiences and is closer to Cusco (1-hour flight). Iquitos provides deeper Amazon immersion with 4-7 day river cruises but requires flying via Lima. Book Amazon accommodations 6-8 weeks ahead.
  3. Plan your altitude acclimatization. Arrive in Cusco at least 2 days before attempting Machu Picchu. Consider flying Lima to Cusco on day 3 of your trip after low-altitude Amazon time, or build in 3 full Cusco acclimatization days if going directly from Lima.
  4. Structure your 14-day flow. Option A - Amazon first: Lima (2 days) → Puerto Maldonado (3-4 days) → Cusco/Sacred Valley (6-7 days) → Lima (1 day). Option B - Cusco first: Lima (2 days) → Cusco region (7-8 days) → Iquitos Amazon (4-5 days) → Lima (1 day).
  5. Book internal flights early. Reserve Lima-Cusco, Lima-Puerto Maldonado, or Lima-Iquitos flights 6-10 weeks ahead. LATAM and Avianca have the most reliable schedules. Morning flights reduce weather delays.
  6. Plan Sacred Valley logistics. Base in Ollantaytambo (closer to Machu Picchu) or Cusco (more services). Book the train to Aguas Calientes 4-6 weeks ahead - PeruRail or Inca Rail. The Vistadome service offers good value.
How far in advance should I book Machu Picchu?
Book 2-4 months ahead, especially for May-September dry season. Huayna Picchu mountain climb tickets sell out even faster and should be booked as soon as available.
Is altitude sickness really a problem in Cusco?
Yes. Cusco sits at 11,200 feet. Most visitors experience some symptoms. Arrive 2-3 days early, avoid alcohol, drink lots of water, and consider prescription medication like acetazolamide.
Which is better for the Amazon - Puerto Maldonado or Iquitos?
Puerto Maldonado is easier logistics (1-hour flight from Cusco) with good wildlife viewing. Iquitos offers deeper jungle immersion but requires flying via Lima. Choose based on your time and adventure level.
Can I do this itinerary in reverse order?
Yes. Starting with Cusco/Machu Picchu then ending with Amazon works well too. The key is allowing enough acclimatization time in Cusco regardless of when you visit.